Purification of ribonuclease T1

An improved method for purifying ribonuclease T1 from Aspergillus oryzae is described. The method uses gradient elution from DEAE-cellulose and sulfopropyl-Sephadex columns followed by gel filtration on Sephadex G-50 to give almost 100 mg (50% yield) of ribonuclease T1 from 100 g of starting material in less than 5 days.     

Trifluoroethanol effects on helix propensity and electrostatic interactions in the helical peptide from ribonuclease T1.

Trifluoroethanol (TFE) is often used to increase the helicity of peptides to make them usable as models of helices in proteins. We have measured helix propensities for all 20 amino acids in water and two concentrations of trifluoroethanol, 15 and 40% (v/v) using, as a model system, a peptide derived from the sequence of the alpha-helix of ribonuclease T1. There are three main conclusions from our studies. (1) TFE alters electrostatic interactions in the ribonuclease T1 helical peptide such that the dependence of the helical content on pH is lost in 40% TFE. (2) Helix propensities measured in 15% TFE correlate well with propensities measured in water, however, the correlation with propensities measured in 40% TFE is significantly worse. (3) Propensities measured in alanine-based peptides and the ribonuclease T1 peptide in TFE show very poor agreement, revealing that TFE greatly increases the effect of sequence context.     

Evidence for a substrate-binding subsite in ribonuclease T1. Crystal structure of the complex with two guanosines, and model building of the complex with the substrate guanylyl-3',5'-guanosine

The enzyme ribonuclease T1 cleaves single-stranded RNA at the 3'-side of guanosine. The structure of the complex with two guanosines has been analyzed at 1.8-A resolution and refined to a crystallographic R value of 14.0%. One guanosine occupies the guanosine recognition site as observed in previously analyzed complexes of ribonuclease T1 with guanosine phosphates. The other is bound to a base-unspecific subsite marking the binding locus of the nucleoside 3'-proximal to guanosine in a cleavable RNA chain. The positions of the guanosine bound to the recognition site and of the guanine base at the subsite were used to guide model building of the substrate guanylyl-3',5'-guanosine bound to the active site of ribonuclease T1. After energy minimization and a 7-ps stochastic dynamics simulation, a plausible model of the enzyme-substrate complex was obtained which may serve as a reference point in consideration of the mechanisms of RNA hydrolysis by ribonuclease T1.     

Comparison between the ribosomal ribonucleic acids from free and membrane-bound ribosomal fractions of HeLa cells.

The rRNA species from the total cytoplasmic, free and membrane-bound fractions of HeLa cells were compared. With the use of T1 ribonuclease and combined T1 ribonuclease plus pancreatic ribonuclease 'fingerprinting' procedures, no significant differences were found between the rRNA species from the different subcellular fractions.     

Domain swapping in ribonuclease T1 allows the acquisition of double-stranded activity

A mutant of ribonuclease T1 (RNase T1), denoted RNase Talpha, that is designed to recognize double-stranded ribonucleic acid was created. RNase Talpha carries the structure of RNase T1 except for a part of its loop L3 domain, which has been swapped for a corresponding domain from alpha-sarcin. The RNase Talpha maintains the pleated beta-sheet structure and retains the guanyl-specific ribonuclease activity of the wild-type RNase T1. A steady-state kinetic study on the RNase Talpha-catalyzed transesterification of GpU dinucleoside phosphates reveals a slightly reduced K(m) value of 6.94 x 10(-7) M. When the stranded specificity is examined, RNase Talpha catalyzes the hydrolysis of guanine base not only of single-stranded but also, as by design, of double-stranded RNA. The change of stranded specificity suggests the feasibility of using domain swapping to make a substrate-specific ribonuclease. This study suggests that the loop L3 in RNase T1 can be used as a 'cassette player' for inserting a functional domain to make ribonuclease of various specificities.     

Protein--RNA interaction in the rat liver 5S rRNA-protein L5 complex studied by digestion with ribonucleases.

Protein-RNA interactions in the 5S rRNA-protein L5 complex from rat liver ribosomes were studied by limited digestion of free and protein bound 5S rRNA with ribonuclease A and T1. In the complex with protein L5 the digestion of 5S rRNA by ribonuclease T1 is decreased at G37 and G89, whereas U38 and C39, and to a lower extent also C10 and U12 become accessible for ribonuclease A.     

Fingerprinting nonradioactive ribonucleic acid with the aid of polynucleotide phosphorylase

We describe a method for obtaining radioactive fingerprints from nonradioactive ribonucleic acid. Fragments derived by T1 ribonuclease digestion of RNA are dephosphorylated with bacterial alkaline phosphatase. When these fragments are used as primers for the reaction of primer dependent polynucleotide phosphorylase with [α-³²P]GDP in the presence of T1 ribonuclease the 3′-hydroxyl group of each fragment becomes phosphorylated. The degree of phosphorylation is reasonably uniform. The method has been applied to T1 ribonuclease digests of Escherichia coli tRNA^Met_f; the oligonucleotides were further analyzed by spleen phosphodiesterase digestion. In a similar manner fingerprints of pancreatic ribonuclease digests of RNA can be obtained, when [α-³²P]UDP, polynucleotide phosphorylase and pancreatic ribonuclease are used.     

Trypanosoma brucei: calcium-dependent endoribonuclease is associated with inhibitor protein

T. brucei cytoplasmic calcium-dependent alkaline ribonuclease activity from DEAE-cellulose fractionation was separated into endoribonuclease and exoribonuclease activities by hydroxyapatite chromatography. T. brucei cytoplasmic extract markedly decreased the endoribonuclease activity, but slightly potentiated the activities of the exoribonuclease and bovine ribonuclease A. While the endoribonuclease was activated by trypsin, the exoribonuclease and bovine ribonuclease A were partially inactivated by trypsin. The endoribonuclease was activated by p-chloromercuribenzoate or N-ethylmaleimide; the exoribonuclease was not affected by these sulfhydryl group reagents. Free ribonuclease was separated from the latent endoribonuclease by 1 M NaCl-Sephadex G-100 gel filtration. The results demonstrate that T. brucei cytoplasm contains a latent endoribonuclease consisting of ribonuclease and inhibitor protein.     

The primary structure of rabbit, calf and bovine liver tRNAPhe.

Highly purified tRNAPhe from rabbit liver, calf liver and bovine liver were completely digested with pancreatic ribonuclease and ribonuclease T1. The oligonucleotides were separated and identified. The tRNAPhe from rabbit liver and calf liver were partially cleaved with ribonuclease T1 or by action of lead acetate. We describe the analyses of the large fragments and the derivation of the primary structure of these mammalian tRNAsPhe.     

Isozymes of ribonuclease and the changes in their relative levels during development in the cellular slime mould Dictyostelium discoideum

The isozymes of ribonuclease were analyzed in cell-free, crude extracts of Dictyostelium discoideum by activity staining of polyacrylamide gels after electrophoresis. The relative levels of three isozymes were then examined during the growth and during the first stages of multicellular development. We observed the replacement of two of these three isozymes by two other isozymes at the pseudoplasmodial stage. These isozymes were different from ribonuclease T1 in terms of their mobility in polyacrylamide gels during electrophoresis. The mobilities of two of the isozymes, DdI and DdII, were 59 and 42% of that of ribonuclease T1. The changes in the relative levels of the isozymes during development are discussed.     

Expression of the chemically synthesized gene for ribonuclease T1 in Escherichia coli using a secretion cloning vector

The gene for ribonuclease T1 from Aspergillus oryzae has been chemically synthesized using the segmental support technique. An Escherichia coli clone producing the ribonuclease at high levels was constructed by linking the gene downstream to the region coding for the signal peptide of the OmpA protein (a major outer membrane protein of E. coli), using the secretion cloning vector pIN-III-ompA2. This strategy was employed in order to circumvent a possible toxic effect of the gene product on the host cell. Active ribonuclease containing four additional amino acids at the N-terminus could be isolated from the periplasmic fraction of the host. The final yield after purification was 20 mg enzyme/l liquid culture. With respect to immunological, catalytic and specific behaviour, no qualitative differences could be detected between the enzyme from the over-producing E. coli strain and ribonuclease T1 isolated from A. oryzae.     

Ribonuclease inhibitor from pig brain: purification, characterization, and direct spectrophotometric assay

The ribonuclease inhibitor from pig brain has been purified 1,500-fold by a combination of ammonium sulfate fractionation, ion-exchange chromatography, hydroxylapatite chromatography, and gel filtration. The inhibitor has a Mr 50,000. It is a noncompetitive inhibitor for pancreatic ribonuclease A with a Ki of 1 nM, forming a 1:1 complex. Both ribonuclease A and B, but not ribonuclease U1 and T1, are inactivated by the inhibitor. The inhibition capacity was abolished by sulfhydryl reagents such as p-chloromercuribenzoate. Incubation of the enzyme-inhibitor complex with the sulfhydryl reagent caused dissociation into active ribonuclease and inactive inhibitor. Dithiothreitol was required during purification to retain the activity of the inhibitor.     

Evidence for rapid association-dissociation of ribonuclease T1 from a recombinant strain of Escherichia coli

On the basis of photon correlation experiments and computer simulations, we provide evidence for a rapid dimerization of the enzyme ribonuclease T1 isolated from an Escherichia coli overproducing strain. An attractive potential in addition to the usual repulsive hardcore and electrostatic potentials was found to be necessary for interpreting the concentration dependence of the diffusion coefficient of the enzyme. Computer searches of surface complementarity suggest that dimer formation of ribonuclease T1 takes place due to an extensive surface contact of approximately 700 A2. Energy minimization of the ribonuclease T1 dimer shows that large conformational changes are not induced upon self-association of the enzyme. The two molecules in the dimer are orientated back-to-back, and this is expected to lead to an active enzyme form.     

Two-dimensional 1H-NMR investigation of ribonuclease T1. Resonance assignments, secondary and low-resolution tertiary structures of ribonuclease T1

Ribonuclease T1 was studied by two-dimensional 1H-NMR spectroscopy. Resonance assignments were obtained for the backbone protons of 95 amino acid residues and most of its side-chain protons using sequence-specific assignment procedures. The secondary structure elements of ribonuclease T1 were identified by an investigation of medium- and long-range nuclear Overhauser effects between the backbone and C beta protons. A low-resolution three-dimensional structure of ribonuclease T1 was deduced from qualitative interpretation of long-range nuclear Overhauser effects.     

Localization of the ribonucleotide sites in rat liver mitochondrial deoxyribonucleic acid.

Supercoiled rat liver mitochondrial DNA is relaxed by treatment with ribonucleases A, T1 or H. All the supercoiled mitochondrial DNA is sensitive to ribonuclease H and ribonuclease A, but only 35% of the supercoiled population is sensitive to ribonuclease T1. Removal of the ribonucleotides with calf thymus ribonuclease H, followed by denaturation of the mitochondrial DNA and analysis of the single-strand fragment lengths in the electron microscope, showed that the ribonucleotides were randomly located on both strands of the DNA. Endonuclease-S1 digestion of mitochondrial DNA after removal of the ribonucleotides reveals that no unique fragments are produced and ribonucleotides are randomly distributed with respect to one another. The average number of ribonucleotide sites per molecule was estimated to be between 8 and 13. Two possible mechanisms for the origin of ribonucleotide sites are discussed.     

Picosecond time-resolved fluorescence of ribonuclease T1. A pH and substrate analogue binding study.

The tryptophyl fluorescence of ribonuclease T1 decays monoexponentially at pH 5.5, tau = 4.04 ns but on increasing pH, a second short-lived component of 1.5 ns appears with a midpoint between pH 6.5 and 7.0. Both components have the same fluorescence spectrum. Acrylamide quenches both fluorescence components, and the short-lived component is quenched fivefold faster than the predominant long component. Binding of the substrate analogue 2'-guanylic acid at pH 5.5 quenches the fluorescence by 20% and introduces a second decay component, tau = 1.16 ns. Acrylamide quenches both tryptophyl decay components, with similar quenching rates. The fluorescence anisotropy decay of ribonuclease T1 was consistent with a molecule the size of ribonuclease T1 surrounded by a single layer of water at pH 7.4, even though the anisotropy decay at pH 5.5 deviated from Stokes-Einstein behavior. The fluorescence data were interpreted with a model where the tryptophyl residue exists in two conformations, remaining in a hydrophobic pocket. The acrylamide quenching is interpreted with electron transfer theory and suggests that one conformer has the nearest atom approximately 3 A from the protein surface, and the other, approximately 2 A.     

Purification of ribonuclease T1 by diethylaminoethylcellulose chromatography

A procedure is described for isolating the enzyme ribonuclease T(1) from Takadiastase, an extract of the mould Aspergillus oryzae. It involves an initial concentration of the enzyme by adsorption on DEAE-cellulose followed by gradient elution. Later the enzyme is chromatographed on the same adsorbent with an eluent of constant composition. Yields of 350-380mg of ribonuclease T(1) from 500g of Takadiastase were obtained.     

Photoreaction of 8-methoxypsoralen with yeast-tRNAPhe. Identification of the major reaction sites

Yeast tRNAPhe was photoreacted with [3H]8-methoxypsoralen and the product was digested with ribonuclease T1, ribonuclease A or a combination of the two or cleaved with sodium borohydride/aniline. The oligonucleotides from these digestions were analyzed by polyacrylamide gel electrophoresis or high-pressure liquid chromatography and the psoralen-containing fragments were identified. The results indicate that one major and two minor photoreaction sites for 8-methoxypsoralen exist in yeast tRNAPhe. The major site (containing about 55% of the label) was determined as U50 in the T psi arm of the tRNA molecule while the minor sites were assigned to U59 (30% of the label) and C70 (15%) respectively. Our results suggest that psoralens may be used as photoprobes for studying conformational changes in tRNA molecules.     

Modification of Glu 58, an amino acid of the active center of ribonuclease T1, to Gln and Asp

Glu 58 is one of the amino acids which participates in its catalytic action of ribonuclease T1. We mutated this residue to Gln 58 or Asp 58 by genetic engineering using chemically synthesized genes. The mutant enzymes were expressed in E. coli as fused proteins and purified to homogeniety on SDS-PAGE after cleavage with cyanogen bromide. Their activities in hydrolyzing pGpC were reduced to 10% in the Asp 58 mutant and about 1% in the Gln 58 mutant compared to that of the wild-type enzyme. These results suggest that Glu 58 is important but not essential for catalysis of ribonuclease T1.     

Ribose recognition by ribonuclease T1: difference spectral binding studies with guanosine and deoxyguanosine.

The binding of ribonuclease T1 with guanosine (Guo) and deoxyguanosine (dGuo) was studied in experiments employing ultraviolet difference spectroscopy in the pH range 3-9 at 0.2 M ionic strength and 25 degrees C. Similar experiments were also conducted with psi-carboxymethyl-glutamate-58 ribonuclease T1 at pH 5.0. At most pH values the characteristic difference spectrum and association constant were obtained. The binding constant for dGuo was approximately 550 M-1 and did not significantly vary in the pH range 3.5-9.0. The binding constant for Guo increased from pH 3.5 to 5.0, was constant between pH 5.0 and 7.0 (approximately 3200 M-1), and decreased at higher pH values. The binding of Guo and dGuo with ribonuclease T1 could also be distinguished in terms of the wavelength for maximal difference absorbance, lambdamax, between pH 5.0 and 7.0. At higher and lower pH values, lambdamax for Guo approached that found fr dGuo. On the other hand, the value of the binding constant (approximately6500 M-1) and the nature of the difference spectra for Guo and dGuo binding with lambdamax-carboxymethyl-glutamate-58-ribonuclease T1 at pH 5.0 were identical. These results suggest that the discrete interaction of the Guo 2'-hydroxyl group with ribonuclease T1 involves the lambda-carboxylate of glutamate-58 and an imidazolium group at the active site.