Porcine thyroid cytosolic, latent alkaline ribonuclease: resistance to protein denaturants.

1. A ribonuclease isolated from porcine thyroid cytosol using phenol: sodium dodecylsulfate treatment was associated with RNA and identical to latent alkaline ribonuclease. 2. Distribution of activity between aqueous and phenolic phases depended on pH, RNA, and ribonuclease inhibitor. 3. The ribonuclease was totally resistant to urea, guanidinium: HCl, chloroform:isoamyl alcohol, ethanol, heating at 100 degrees C for 10 min or at 80 degrees C plus 100 mM NaCl. It was highly resistant to hydrolysis by proteinase K except in the presence of detergent. 4. The extreme stability and other properties of latent alkaline ribonuclease could be the result of its association with RNA.     

Demethylation of DNA by purified chick embryo 5-methylcytosine-DNA glycosylase requires both protein and RNA.

We have previously purified and characterized a 5-methylcytosine (5-MeC)-DNA glycosylase from 12 day old chick embryos [Jost,J.P. et al. (1995) J. Biol. Chem. 270, 9734-9739]. The activity of the purified enzyme is abolished upon treatment with proteinase K and ribonuclease A. RNA copurifies with 5-MeC-DNA glycosylase activity throughout all chromatographic steps and preparative gel electrophoresis. RNA with a length of approximately 300-500 nucleotides was isolated from the gel purified enzyme. Upon extensive treatment with proteinase K, the gel eluted and labeled RNA did not show any significant change in molecular mass. The purified RNA incubated alone or in the presence of Mg2+and deoxyribonucleotide phosphates had no 5-MeC-DNA glycosylase or demethylating activities. However, activity of 5-MeC-DNA glycosylase could be restored when the purified RNA was incubated with the inactive protein, free of RNA.     

A note on the use of urea in studying the mechanism of thermal inactivation of extracellular proteinase from pseudomonas fluorescens 22F

Strong denaturants can be used to distinguish between heat-induced changes in the primary structure of the enzyme molecule and heat-induced changes in higher orders of structure. In this paper, we report on an attempt to use urea in studying the mechanism of thermal inactivation of the extracellular proteinase from Pseudomonas fluorescens 22F. Addition of urea at> 2 (without heating) resulted in inactivation which was, however, reversible. Diluting to concentrations < 2 urea completely restored proteolytic activity. The rate of inactivation at 100°C of the proteinase was increased when 6 urea was present during heat treatment. Also at lower urea concentrations, the inactivation rate at 100°C was increased. Addition of 6 urea to the enzyme solution after heat treatment also increased the extent of inactivation while low urea concentrations (< 1 ) did not. It was concluded that cyanate formed from urea at high temperature was the cause of increased inactivation since addition of cyanate could increase the inactivation rate while a treatment to remove cyanate from a heated urea solution could prevent increase tnactivation. The use of urea does not appear to be suitable for the elucidation of the mechanism of thermal inactivation of the extracellular proteinase from P. fluorescens 22F, but might be applicable to other enzymes when treated (cyanate free) urea is used after heat treatment; however, use of urea (even if cyanate free) during heat treatment is not possible because cyanate is induced by the very heat treatment.     

A simple method of characterizing mitochondrial ribonucleic acid.

A simple method of isolating and characterizing RNA from L-cell mitochondria is described. The mitochondrial fraction is lysed by sodium dodecyl sulphate, and the RNA fractionated by sucrose-density-gradient centrifugation. The efficacy of proteinase K in preventing ribonuclease activity is also demonstrated.     

Tests of the simple model of Lin and Brandts for the folding kinetics of ribonuclease A

L.-N. Lin and J.F. Brandts recently proposed a simple model for the folding kinetics of ribonuclease A in which folding intermediates are not detectable. We have tested the basic assumption of the simple model for the major unfolded species, which is produced by a slow isomerization (the "X in equilibrium Y reaction" according to Lin and Brandts) after unfolding. The simple model assumes that in refolding the slow Y----X reaction must occur before any folding can take place. We have measured the Y----X reaction during folding. Tyrosine-detected folding occurs before the Y----X reaction; the difference in rate between the Y----X reaction and folding monitored by tyrosine absorbance becomes large when the stabilizing salt 0.56 M (NH4)2SO4 is added. The simple model predicts that the kinetic properties of the X in equilibrium Y reaction in unfolded ribonuclease are the same as those of tyrosine-detected folding. We find, however, that the kinetics of the X in equilibrium Y reaction in unfolded ribonuclease are independent of urea concentration, whereas the rate of tyrosine-detected folding decreases almost 100-fold between 0.3 and 5 M urea, as reported by Lin and Brandts. We point out that the kinetic properties of the X in equilibrium Y reaction in unfolded ribonuclease are characteristic of proline isomerization.     

On the efficacy of commonly used ribonuclease inhibitors.

The ability of a number of commonly used inhibitors to inhibit pancreatic ribonuclease has been studied. At ribonuclease concentrations of 10 or 100 g/ml, heparin, polyvinylsulfate and proteinase K, at concentrations reported for their use in the literature, were ineffective in inhibiting RNase digestion of ³H-uridine labelled RNA from $\text{Streptomyces antibioticus}$. In contrast, macaloid, diethylpyrocarbonate and sodium dodecyl sulfate were all effective inhibitors, with the degree of effectiveness decreasing in the order stated. Further, at inhibitor concentrations which allowed RNase conversion of only 50% of the labelled RNA to acid soluble products, a larger percentage of the acid insoluble digestion products sedimented in the “high molecular weight” range (4–16s) when macaloid was the inhibitor used than when diethylpyrocarbonate was the inhibitor.     

Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin-Dahlem, GFR.

It is well established that when E. coli 30S ribosomal subunits are irradiated with ultraviolet light under mild conditions a specific cross-link is formed between protein S7 and the 16S RNA. Methodology is presented for the analysis of the single nucleotide residue concerned in this cross-link. Firstly, the identity of the ribonuclease T1 octanucleotide attached to S7 is confirmed by a new method, which involves isolation and analysis of S7-polynucleotide complexes containing 30 -- 40 nucleotides. Secondly, the isolated S7-octanucleotide complex is digested successively with ribonuclease A, proteinase K and ribonuclease T2, and the nucleotides liberated are identified. The results show unambiguously that uridine residue number 1239 in the 16S RNA sequence is cross-linked to protein S7.     

Characterization of an in vitro assay for import of 3-phosphoglycerate kinase into the glycosomes of Trypanosoma brucei.

Glycosomes are microbody organelles found in kinetoplastida, where they serve to compartmentalize the enzymes of the glycolytic pathway. In order to identify the mechanism by which these enzymes are targeted to the glycosome, we have modified the in vitro import assay developed by Dovey et al. (Proc. Natl. Acad. Sci. USA 85:2598-2602, 1988). This assay measures the uptake of in vitro-translated Trypanosoma brucei glycosomal 3-phosphoglycerate kinase (gPGK) by purified glycosomes. Up to 50% of the total 35S-gPGK in the glycosomal fraction was resistant to extraction by 3 M urea or treatment with proteinase K (500 micrograms/ml). The glycosome-associated 35S-gPGK could be chemically cross-linked to the endogenous glycosomal proteins to form a sodium dodecyl sulfate-resistant complex, suggesting that it is close to the intraglycosomal protein matrix. Deoxycholate solubilized the glycosome and thereby rendered the glycosome-associated 35S-gPGK fully susceptible to proteinase K. However, the glycosome-associated 35S-gPGK was not digested by proteinase K in the presence of Triton X-100, which cannot dissolve the glycosomal protein core. The 35S-gPGK synthesized in vitro was able to bind directly to protein cores, where it became resistant to urea extraction and proteinase K digestion. However, the 35S-gPGK-protein core complex exhibited a much higher density than the 35S-gPGK-glycosome complex and was readily separable in sucrose gradients. Thus, in our in vitro import assay, the 35S-gPGK appeared to associate with intact glycosomes, possibly reflecting import of protein into the organelle. Complete denaturation of the 35S-gPGK in 8 M urea prior to the assay enhanced the efficiency of its association with glycosomes. Native gPGK did not compete with the association of in vitro-translated gPGK unless it was denatured. The assay exhibited time and temperature dependence, but it did not require externally added ATP and was not inhibited by the nonhydrolyzable analogs adenosine-5'-(beta,gamma-imido)-triphosphate and gamma-S-ATP. However, the presence of 20 to 30 microM ATP inside the glycosome may fulfill the requirement for protein import.     

Isolation of undegraded polysomes from radish cotyledons: Use of proteinase K and cycloheximide

A procedure for isolating undegraded polysomes from radish cotyledons is described. The current method for plant polysome preparation using buffers of high pH and high ionic strength was unable to prevent the breakdown of large polysomes occurring during the extraction. Proteinase K was very efficient in protecting polysomes from degradation. However, this yielded a high monosome content in the preparations. When proteinase K was combined with cycloheximide, a more satisfactory recovery of polysomes was achieved. This procedure could facilitate investigations of the in vitro protein synthesis activity and mRNA isolation in tissues possessing a high ribonuclease content.     

Effect of stagnant hypoxia on acid ribonuclease activity in the rat prosencephalon during ontogenesis.

In the rat prosencephalon it proved possible to differentiate lysosomal ribonuclease from alkaline ribonuclease activity, which could be detected only in the presence of p-chlormercuribenzoate. Acid RNase activity related to the amount of protein in the prosencephalon fell during ontogenesis. It was not significantly affected by four hours' stagnant hypoxia induced by ligation of both carotids. Its release from the lysosomes rose, however (when isotonic homogenates were spun at 20,000 g, acid ribonuclease activity in the supernatants was elevated). The absence of correlation between this activation and the degree of maturity of the nervous tissue refutes the hypothesis that regulation of this enzyme is per se responsible for the known changes induced by hypoxia in the RNA content of the prosencephalon of rats of different ages. On the contrary, the results indirectly support studies which demonstrate changes in the extent of RNA synthesis after hypoxia.     

The occurrence and distribution of poly(a) ribonucleic Acid in soybean

The occurrence and distribution of poly(A) sequences in the RNA of soybean (Glycine max var. Wayne) have been studied. Only one of the two species of AMP-rich RNA contains poly(A). D-RNA does not contain detectable poly(A) sequences. The TB-RNA is the poly(A) RNA in this system. At least a part (up to 50% or more) of the mRNA in polyribosomes contains a poly(A) sequence. The poly(A) RNA is heterodisperse in size but has a mean size of approximately 18S (2,000 nucleotides) in urea and formamide gels. The poly(A) fragment resulting from ribonuclease A and T₁ digestion migrates as a broad band overlapping the 4 to 5.8S regions of the gels with a mean size of somewhat greater than 5S. No evidence was found for the occurrence of a discrete oligo(A) fragment in the poly(A) RNA; however, oligonucleotides which migrate faster than the poly(A) fraction were observed in preparations which were not bound to oligo(dT) cellulose prior to electrophoresis. This oligonucleotide region was enriched in AMP (up to about 65%) as would be expected after ribonuclease A and T₁ digestion.     

Protein interactions with surface-immobilized metal ions: structure-dependent variations in affinity and binding capacity with temperature and urea concentration.

We have used equilibrium binding analyses to evaluate the influence of temperature and urea on the affinity of hen egg white lysozyme and bovine pancreatic ribonuclease A for surface-immobilized Cu(II) ions. Linear Scatchard plots suggested that these model proteins were interacting with immobilized metal ions via a single class of intermediate-affinity (Kd = 10-40 microM) binding sites. Alterations in temperature had little or no effect on the immobilized Cu(II) binding capacity of either protein. Temperature effects on the interaction affinity, however, were protein-dependent and varied considerably. The affinity of lysozyme for immobilized Cu(II) ions was significantly decreased with increased temperature (0 degree C-37 degrees C), yet the affinity of ribonuclease did not vary measurably over the same temperature range. The van 't Hoff plot (1n K vs 1/T) for lysozyme suggests a straight line relationship (single mechanism) with a delta H of approximately -5.5 kcal/mol. Urea effects also varied in a protein-dependent manner. A 10-fold reduction in the affinity of lysozyme for the immobilized Cu(II) was observed with the urea concentrations up to 3 M; yet urea had no effect on the affinity of ribonuclease for the immobilized metal ions. Although the interaction capacity of lysozyme with the immobilized Cu(II) ions was decreased by 50% in 3 M urea, ribonuclease interaction capacity was not diminished in urea. Thus, temperature- and urea-dependent alterations in protein-metal ion interactions were observed for lysozyme but not ribonuclease A. The complete, yet reversible, inhibition of lysozyme- and ribonuclease-metal ion interactions by carboxyethylation with low concentrations of diethylpyrocarbonate provided direct evidence of histidyl involvement. The differential response of these proteins to the effects of temperature and urea was, therefore, interpreted based on calculated solvent-accessibilities and surface distributions of His residues, individual His residue pKa values, and specific features of the protein surface structure in the immediate environment of the surface-exposed histidyl residues. Possible interaction mechanisms involved in protein recognition of macromolecular surface-immobilized metal ions are presented.     

Latent proteinase activity of gamma-glutamyl transpeptidase light subunit.

gamma-Glutamyl transpeptidase, which is composed of two unequal subunits, exhibits proteinase activity when treated with agents such as urea and sodium dodecyl sulfate. The heavy subunit is preferentially and rapidly degraded. The enzyme also degraded bovine serum albumin in the presence of urea; however, several other proteins and model proteinase substrates were not cleaved. Treatment of the enzyme with 6-diazo-5-oxo-L-norleucine, a gamma-glutamyl analog, results in parallel loss of transpeptidase and proteinase activities indicating that the site at which gamma-glutamylation of the enzyme occurs (presumably a hydroxyl group on the light subunit) is also involved in proteinase activity. The purified light subunit, but not the heavy subunit, exhibits proteinase activity even in the absence of urea. Results suggest that dissociation of the enzyme unmasks the proteinase activity of the light subunit involving the site at which gamma-glutamylation of the enzyme occurs, and that the heavy subunit may impose transpeptidase reaction specificity by contributing the binding domains for gamma-glutamyl substrates.     

Pyrogenic Principle of the Ribonucleic Acid from the Yeast Candida utilis

Experiments were performed to characterize the pyrogenic principle of ribonucleic acid (RNA) from the yeast Candida utilis. It was shown that ribonuclease hydrolysis of the RNA does not lead to inactivation of the pyrogenicity. Pyrogenicity was, however, destroyed by treatment with sodium deoxycholate. On column chromatography with Biogel under sterile and pyrogen-free conditions, the pyrogenic principle of yeast RNA was eluted together with the RNA. After treatment of the RNA with ribonuclease, it was possible to separate the pyrogenic activity from the RNA (hydrolysis products) to a great extent. Column chromatography of Escherichia coli endotoxin showed that the endotoxin was eluted in the same fractions as the pyrogenic activity of yeast RNA. On the basis of the behavior of the pyrogen, it may very well be that the fever reaction is produced not by the nucleic acid but by pyrogenic contaminants of the RNA preparation.     

Proteolytic cleavage of the puromycin-sensitive aminopeptidase generates a substrate binding domain

The puromycin-sensitive aminopeptidase was found to be resistant to proteolysis by trypsin, chymotrypsin, and protease V8 but was cleaved into an N-terminal 60-kDa fragment and a C-terminal 33-kDa fragment by proteinase K. The two proteinase K fragments remain associated and retained enzymatic activity. Attempts to express the 60-kDa N-terminal fragment in Escherichia coli produced inclusion bodies. A hexa-histidine fusion protein of the 60-kDa N-terminal fragment was solubilized from inclusion bodies with urea and refolded by removal of the urea through dialysis. The refolded protein was devoid of aminopeptidase activity as assayed with arginine-beta-naphthylamide. However, the refolded protein bound the substrate dynorphin A(1-9) with a stoichiometry of 0.5 mol/mol and a K(0.5) value of 50 microM. Dynorphin A(1-9) binding was competitively inhibited by the substrate dynorphin B(1-9), but not by des-Tyr(1)-leucine-enkephalin, a poor substrate for the enzyme.     

Impact of altered protein structures on the intracellular traffic of a mutated vasopressin precursor from Brattleboro rats

The rat vasopressin precursor, synthesized in the reticulocyte lysate system under the direction of in vitro transcribed mRNA, is processed and correctly delivered to the lumen of added microsomal vesicles. Translation of mRNA for the mutant (Brattleboro) vasopressin precursor which lacks a translational stop codon as a consequence of a frame-shift mutation, gives rise to a mutated protein (B-mutant precursor) with a C-terminal poly(lysine) sequence encoded by the poly(A) tail. Upon addition of microsomal membranes, the mutated precursor has access to the lumen of the vesicles as indicated by removal of the signal peptide; however, the C-terminal part with the poly(lysine) tail remains outside the vesicles as shown by its sensitivity to proteinase K. When a modified RNA, including a stop codon located similarly to that found in the cDNA encoding the normal precursor, is translated in the presence of microsomal membranes, the resulting product (S-mutant precursor) is refractory to proteolysis by exogenously added proteinase K. Analysis of the microsomal membranes indicates, however, that the C-terminus of the S-mutant precursor is still anchored within membranes. For studying the intracellular transport of the mutated precursor Xenopus laevis oocytes were injected with various RNA constructs. To monitor the transport steps from the endoplasmic reticulum to the Golgi compartment an RNA encoding a glycosylation site within the S-mutant precursor sequence was constructed. The resulting GS-mutant precursor is synthesized in the oocyte but not secreted into the incubation medium, completely in contrast to the normal vasopressin precursor which can be detected in the incubation bath 4 h after injection of the respective RNA. The sensitivity of the GS-mutant precursor carbohydrate side chain to endoglycosidase H treatment suggests that the mutated precursor does not reach the Golgi apparatus.     

Characterization of the ribonuclease activity on the skin surface

The rapid degradation of ribonucleic acids (RNA) by ubiquitous ribonucleases limits the efficacy of new therapies based on RNA molecules. Therefore, our aim was to characterize the natural ribonuclease activities on the skin and in blood plasma i.e. at sites where many drugs in development are applied. On the skin surfaces of Homo sapiens and Mus musculus we observed dominant pyrimidine-specific ribonuclease activity. This activity is not prevented by a cap structure at the 5'-end of messenger RNA (mRNA) and is not primarily of a 5'- or 3'-exonuclease type. Moreover, the ribonuclease activity on the skin or in blood plasma is not inhibited by chemical modifications introduced at the 2'OH group of cytidine or uridine residues. It is, however, inhibited by the ribonuclease inhibitor RNasin^® although not by the ribonuclease inhibitor SUPERase· In?. The application of our findings in the field of medical science may result in an improved efficiency of RNA-based therapies that are currently in development.     

Differences in the denaturation behavior of ribonuclease A induced by temperature and guanidine hydrochloride

Moderate temperatures or low concentrations of denaturants diminish the catalytic activity of some enzymes before spectroscopic methods indicate protein unfolding. To discriminate between possible reasons for the inactivation of ribonuclease A, we investigated the influence of temperature and guanidine hydrochloride on its proteolytic susceptibility to proteinase K by determining the proteolytic rate constants and fragment patterns. The results were related to changes of activity and spectroscopic properties of ribonuclease A. With thermal denaturation, the changes in activity and in the rate constants of proteolytic degradation coincide and occur slightly before the spectroscopically observable transition. In the case of guanidine hydrochloride-induced denaturation, however, proteolytic resistance of ribonuclease A initially increases accompanied by a drastic activity decrease far before unfolding of the protein is detected by spectroscopy or proteolysis. In addition to ionic effects, a tightening of the protein structure at low guanidine hydrochloride concentrations is suggested to be responsible for ribonuclease A inactivation.     

Comparative study on proteinase R, T, and K from Tritirachiam album limber

Proteinase R and T purified from Tritirachiam album limber were characterized in comparison with proteinase K using circular dichroism (CD), enzyme activity, thermal melting, and sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE). CD analysis suggested that these three proteins possess some beta-sheet structure, with little alpha-helix except for proteinase R which showed about 14% alpha-helix. SDS-PAGE and gel filtration in 0.1% SDS indicated that proteinase T and K are resistant to SDS-induced unfolding similar to subtilisin. Thermal denaturation experiments showed the melting temperature for proteinase T to be 67 degrees and that for proteinase K to be 65 degrees in the absence of Ca2+, with higher melting temperatures in the presence of Ca2+. However, the enzyme activities of proteinase T and R were significantly lower than those of proteinase K.     

Detection of high levels of polyadenylate-containing RNA in bacteria by the use of a single-step RNA isolation procedure

A new one-step procedure for the isolation of bacterial RNA, involving lysis by proteinase K in the presence of sodium dodecyl sulfate, is described. Pulse-labeled RNA isolated by this procedure for Bacillus brevis, Bacillus subtilis, and Escherichia coli B has been found to contain a substantial fraction (15-40%) of polyadenylated RNA as determined by adsorption to oligo(dT)-cellulose. This contrasts with RNA isolated by procedures involving phenol extraction, a process which appears to lead to the selective loss of polyadenylated RNA. The presence of polyadenylated RNA in E. coli was confirmed by an independent method which involved hybridization with [3H]polyuridylic acid. Using the proteinase K method for RNA isolation, it was possible to demonstrate the in vitro synthesis of polyadenylated RNA by toluene-treated cells of B. brevis, B. subtilis, and E. coli.