Studies on extracellular ribonucleases of Ustilago sphaerogena. Characterization of substrate specificity with special reference to purine-specific ribonucleases

1. Ribonuclease U(1) splits only the phosphodiester bonds of guanosine 3'-phosphates in RNA. It may be regarded as a guanyloribonuclease [ribonucleate (guanine nucleotide)-2'-transferase (cyclizing), EC 2.7.7.26] similar to ribonuclease T(1) (Egami, Takahashi & Uchida, 1964). It seems to be identical with the extracellular ribonuclease described by Glitz & Dekker (1963, 1964a,b). 2. Ribonucleases U(2) and U(3) are novel enzymes with a strict specificity. They split the internucleotide bonds between purine 3'-nucleotides and 5'-hydroxy groups of adjacent nucleotides in RNA with the intermediary formation of purine nucleoside 2',3'-(cyclic)-phosphates, which are slowly hydrolysed to purine 3'-nucleotides. So they may be classified as ;puryloribonucleases [ribonucleate (purine nucleotide)-2'-transferase (cyclizing)]'. Double-stranded RNA is scarcely split by ribonucleases U(2) and U(3). 3. Ribonuclease U(4) has no absolute base specificity, and produces the mononucleotides 3'-adenylate, 3'-guanylate, 3'-cytidylate and 3'-uridylate from RNA.     

A distinctive ribonuclease from fresh fruiting bodies of the medicinal mushroom Ganoderma lucidum

A ribonuclease with an N-terminal sequence distinct from other mushroom ribonucleases was isolated from fresh fruiting bodies of the medicinal mushroom Ganoderma lucidum. The ribonuclease was adsorbed on DEAE-cellulose and Q-Sepharose, and unadsorbed on CM-Sepharose. It possessed a molecular mass of 42 kDa as judged by gel filtration by fast protein liquid chromatography on Superdex 75 and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Its molecular mass was similar to that of straw mushroom ribonuclease but much higher compared with those of other mushroom ribonucleases. The ribonuclease was unique among mushroom ribonucleases in that it exhibited the highest potency toward poly(U), followed by poly(A). Its activity toward poly(G) and poly(C) was about one-half of that toward poly(A) and one-quarter of that toward poly(U). A pH of 4.0 and a temperature of 60 degrees C were required for optimal activity of the enzyme. The optimum pH was low compared with those reported for other mushroom ribonucleases.     

Purification and characterization of bovine aorta ribonucleases

1. Two ribonucleases (aorta ribonuclease I and aorta ribonuclease II) from bovine aorta were purified 4611-fold and 667-fold respectively. Ethanolic precipitation, acid extraction, isoionic precipitation at pH3.5 and Bio-Rex 70 column chromatography were the methods employed. 2. Aorta ribonuclease I exhibited no deoxyribonuclease or alkaline phosphatase activity. 3. Aorta ribonuclease I appeared to be homogeneous when subjected to discontinuous gel electrophoresis. 4. Aorta ribonuclease II exhibited the same properties as aorta ribonuclease previously isolated. 5. The activities of the aorta ribonucleases and pancreatic ribonuclease on homopolymers and dinucleoside phosphates were compared. 6. Aorta ribonuclease I exhibited optimum pH7.5 and, under the assay conditions used, optimum temperature 60 degrees .     

Rapid Diversification of RNase A Superfamily Ribonucleases from the Bullfrog, Rana catesbeiana

We present sequences of five novel RNase A superfamily ribonuclease genes of the bullfrog, Rana catesbeiana. All five genes encode ribonucleases that are similar to Onconase, a cytotoxic ribonuclease isolated from oocytes of R. pipiens. With amino acid sequence data from 14 ribonucleases from three Rana species (R. catesbeiana, R. japonica, and R. pipiens), we have constructed bootstrap-supported phylogenetic trees that reorganize these ribonucleases into five distinct lineages--the pancreatic ribonucleases (RNases 1), the eosinophil-associated ribonucleases (RNases 2, 3, and 6), the ribonucleases 4, the angiogenins (RNases 5) and the Rana ribonucleases--with the Rana ribonucleases no more closely related to the angiogenins than they are to any of the other ribonuclease lineages shown. Further phylogenetic analysis suggests the division of the Rana ribonucleases into two subclusters (A and B), with positive (Darwinian) selection (dN/dS > 1.0) and an elevated rate of radical nonsynonymous substitution (dR) contributing to the rapid diversification of ribonucleases within each cluster. This pattern of evolution-rapid diversification via positive selection among sequences of a multigene cluster-bears striking resemblance to what we have described for the eosinophil-associated ribonuclease genes of the rodent Mus musculus, a finding that may have implications with respect the physiologic function of this unique family of proteins.     

The isolation and partial characterization of ribonuclease A from Bison bison

1. Bison ribonuclease was isolated from pancreas glands of Bison bison by acid extraction, (NH(4))(2)SO(4) fractionation, affinity chromatography on Sepharose-5'-(4-aminophenylphosphoryl)uridine 2',3'-phosphate and ion-exchange chromatography on Bio-Rex-70. 2. The selectivity of the affinity column towards bison ribonuclease in heterogeneous protein solutions was greatly improved by employing piperazine buffers at pH5.3, which decreased non-specific interactions of other proteins. Rapid desorption from the affinity column was obtained with sodium phosphate buffer (pH3). 3. Bison ribonuclease has a total amino acid content very similar to ox ribonuclease. Inactivation of bison ribonuclease with iodoacetic acid leads to the formation of 0.62 residues of pi-carboxymethylhistidine and 0.36 residues of tau-carboxymethylhistidine. The amino acid composition of peptides isolated from diagonal peptide ;maps' and also of peptides isolated after pH1.6 and 2.4 two-dimensional high-voltage electrophoresis of a digest of bison ribonuclease labelled with pyridoxal 5-phosphate indicates that there is complete homology between ox and bison ribonucleases. 4. The Schiff-base attachment site of pyridoxal 5-phosphate was identified as lysine-41 by NaBH(4) reduction followed by peptide isolation.     

Purification and cloning of cytotoxic ribonucleases from Rana catesbeiana (bullfrog)

Ribonucleases with antitumor activity are mainly found in the oocytes and embryos of frogs, but the role of these ribonucleases in frog development is not clear. Moreover, most frog ribonuclease genes have not been cloned and characterized. In the present study, a group of ribonucleases were isolated from Rana catesbeiana (bullfrog). These ribonucleases in mature oocytes, namely RC-RNase, RC-RNase 2, RC-RNase 3, RC-RNase 4, RC-RNase 5 and RC-RNase 6, as well as liver-specific ribonuclease RC-RNase L1, were purified by column chromatographs and detected by zymogram assay and western blotting. Characterization of these purified ribonucleases revealed that they were highly conserved in amino acid sequence and had a pyroglutamate residue at their N-termini, but possessed different specific activities, base specificities and optimal pH values for their activities. These ribonucleases were cytotoxic to cervical carcinoma HeLa cells, but their cytotoxicities were not closely correlated to their enzymatic specific activities. Some other amino acid residues in addition to their catalytic residues were implicated to be involved in the cytotoxicity of the frog ribonucleases to tumor cells. Because the coding regions lack introns, the ribonuclease genes were cloned by PCR using genomic DNA as template. Their DNA sequences and amino acid sequences are homologous to those of mammalian ribonuclease superfamily, ~50 and ~25%, respectively.     

A ribonuclease with distinctive features from the wild green-headed mushroom Russulus virescens

A ribonuclease with an N-terminal sequence different from those of other ribonucleases has been purified from fruiting bodies of the mushroom Russula virescens. The RNase was adsorbed on DEAE-cellulose and Q-Sepharose in 10mM Tris-HCl buffer (pH 7.1-7.3) and on CM-Sepharose in 10mM NH(4)OAc buffer (pH 4.6), unlike other mushroom ribonucleases which are unadsorbed on DEAE-cellulose. The RNase demonstrated a molecular mass of 28kDa in both gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In contrast to other mushroom ribonucleases which are monospecific, it exhibited co-specificity towards poly A and poly C. It demonstrated a pH optimum of 4.5, which is lower than values reported for other mushroom ribonucleases, and a temperature optimum of 60 degrees C.     

Magnesium ion-independent ribonucleic acid depolymerases in bacteria

The distribution of ribonucleases among bacteria has been determined from the examination of a wide variety of species. Bacteria that had been growing rapidly on a solid medium were harvested, treated with acetone and incubated in the presence of EDTA between pH4 and pH9. The ribonuclease activity was determined from the rate at which acid-soluble nucleotides were released. Out of nearly 200 strains examined, about 30 did not contain a detectable ribonuclease. The pH optima of ribonucleases in the remainder were sufficiently distinctive to suggest a use in taxonomy. Escherichia coli B was examined in more detail to determine the factors responsible for variations in the ribonuclease content of this bacterium. Growth rate had little influence on ribonuclease content when a complex medium containing no readily assimilable carbohydrate was used; the addition of glucose resulted in a marked increase in ribonuclease and a dependence of enzyme content on growth rate. An increase in the concentration of sodium chloride in the medium decreased the ribonuclease content of bacteria growing on it.     

Isolation of a ribonuclease from sanchi ginseng (Panax pseudoginseng) flowers distinct from other ginseng ribonucleases

A single-chained ribonuclease was isolated from the aqueous extract of sanchi ginseng (Panax pseudoginseng) flowers. It exhibited a molecular mass of 23 kDa, an N-terminal sequence with some similarity to other enzymes involved in RNA metabolism but different from known ribonucleases, and considerably higher activity toward poly U than poly C and only slight activity toward poly A and poly G. The purification protocol entailed ion exchange chromatography on diethylaminoethyl (DEAE)-cellulose, affinity chromatography on Affi-gel blue gel, ion exchange chromatography on carboxymethyl (CM)-cellulose, and gel filtration on Superdex 75. The ribonuclease was unadsorbed on DEAE-cellulose and adsorbed on Affi-gel blue gel and CM-cellulose. Maximal activity of the ribonuclease was attained at pH 7. On either side of this pH the enzyme activity underwent a drastic decline. The enzyme activity was at its highest at 50 degrees C and dropped to about 20% of the maximal activity when the temperature was decreased to 20 degrees C or elevated to 80 degrees C. The characteristics of sanchi ginseng flower ribonuclease were different from those of the ribonucleases previously purified from sanchi ginseng and Chinese ginseng roots including ribonuclease from Chinese ginseng flowers which are morphologically very similar to sanchi ginseng flowers.     

Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications

The widespread and functionally varied members of the ribonuclease A (RNase A) superfamily provide an excellent opportunity to study evolutionary forces at work on a conserved protein scaffold. Representatives from the zebrafish are of particular interest as the evolutionary distance from non-ichthyic homologues is large. We conducted an exhaustive survey of available zebrafish DNA sequences and found significant polymorphism among its four known homologues. In an extension of previous nomenclature, the variants have been named RNases ZF-1a-c,-2a-d,-3a-e and-4. We present the first X-ray crystal structures of zebrafish ribonucleases, RNases ZF-1a and-3e at 1.35-and 1.85 Å resolution, respectively. Structure-based clustering with ten other ribonuclease structures indicates greatest similarity to mammalian angiogenins and amphibian ribonucleases, and supports the view that all present-day ribonucleases evolved from a progenitor with three disulphide bonds. In their details, the two structures are intriguing melting-pots of features present in ribonucleases from other vertebrate classes. Whereas in RNase ZF-1a the active site is obstructed by the C-terminal segment (as observed in angiogenin), in RNase ZF-3e the same region is open (as observed in more catalytically efficient homologues). The progenitor of present-day ribonucleases is more likely to have had an obstructive C terminus, and the relatively high similarity (late divergence) of RNases ZF-1 and-3 infers that the active site unblocking event has happened independently in different vertebrate lineages.     

Purification and characterization of a novel UpN-specific endoribonuclease VI from Artemia larvae

Artemia larval ribonuclease (Sebastián, J., and Heredia, C. F., (1978) Eur. J. Bichem. 90, 405-411) has been purified near homogeneity and its properties were studied. It consists of a single polypeptide chain of 38,000 daltons. It requires a divalent cation for activity. Ca2+ is the most effective among the metals tested. The metal dependence of the activity is biphasic. Maximal activity is obtained at 5-10 mM. In the absence of metals and chelating agents in the assay, 30-40% of the activity is observed. However, if chelating agents are added, the activity is abolished. At low concentrations of free metal (1-20 microM), 30-40% of maximal activity is obtained with Ca2+ or Mn2+, but not with Mg2+, Ca2+, but not Mn2+ or Mg2+, protects the enzyme from thermal inactivation. The best substrates for Artemia ribonuclease are poly(U) and poly(A), although with the latter it has only 10% the activity shown with the former. Using poly(U) as substrate, the products of a terminal digestion are P-2':3'-Urd and 3'-UMP. Using dinucleoside monophosphates as substrates, the enzyme is highly specific for a U residue at the 3' side of the phosphodiester bond (UpN), especially UpA, being inactive if the U residue is at the 5' side (NpU). Although some of its properties are similar to other eukaryotic or prokaryotic ribonucleases, its high specificity for UpN bonds suggest that this is a new type of ribonuclease. Moreover, it is a potentially useful enzyme for RNA analysis and/or sequencing.     

pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1

To investigate the pH dependence of the conformational stability of ribonucleases A and T1, urea and guanidine hydrochloride denaturation curves have been determined over the pH range 2-10. The maximum conformational stability of both proteins is about 9 kcal/mol and occurs near pH 4.5 for ribonuclease T1 and between pH 7 and 9 for ribonuclease A. The pH dependence suggests that electrostatic interactions among the charged groups make a relatively small contribution to the conformational stability of these proteins. The dependence of delta G on urea concentration increases from about 1200 cal mol-1 M-1 at high pH to about 2400 cal mol-1 M-1 at low pH for ribonuclease A. This suggests that the unfolded conformations of RNase A become more accessible to urea as the net charge on the molecule increases. For RNase T1, the dependence of delta G on urea concentration is minimal near pH 6 and increases at both higher and lower pH. An analysis of information of this type for several proteins in terms of a model developed by Tanford [Tanford, C. (1964) J. Am. Chem. Soc. 86, 2050-2059] suggests that the unfolded states of proteins in urea and GdnHCl solutions may differ significantly in the extent of their interaction with denaturants. Thus, the conformations assumed by unfolded proteins may depend to at least some extent on the amino acid sequence of the protein.     

Purification of cytosolic,latent endoribonuclease from porcine thyroid

An alkaline endoribonuclease was purified 1800-fold from the cytosolic, latent ribonuclease fraction of porcine thyroids by gentle procedures specifically designed to exclude both heating and acidification steps. Polyacrylamide gel electrophoresis revealed a broad peak of enzyme activity that was coincident with the stained protein band. As estimated by gel filtration chromatography the major form of the enzyme (59%) had a molecular weight of 51,000; the remainder of the activity was distributed among six minor forms. Carboxymethyl-cellulose chromatography showed that the enzyme had at least three interconvertible forms. The latent alkaline ribonuclease had a pH optimum of 8.1 in both Tris and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffers and was stimulated by a number of monovalent chloride and potassium salts at ionic strengths between 10 and 70 mm; above 100 mm the salts were all inhibitory with the exception of ammonium chloride. At 1 mm both MgCl₂ and CaCl₂ were stimulatory, whereas CuCl₂ ZnCl₂ and EDTA were inhibitors. Both native and denatured DNA were slightly stimulatory. The porcine thyroid latent alkaline ribonuclease was specific for pyrimidine homopolymers and yielded a mixture of cyclic mononucleotides and oligonucleotides when incubated with poly(C). It did not hydrolyze 2′(3′)-cyclic CMP, purine homopolymers, native or denatured DNA or poly(A) · poly(U). Its activity toward rRNA was greater than toward tRNA and it cleaved the former to a mixture of mononucleotides and oligonucleotides. The properties of the intracellular, cytosolic, latent, alkaline ribonuclease distinguish it from pancreatic ribonuclease A and other nonsecretory ribonucleases.     

Extracellular ribonuclease from Bacillus thuringiensis

The ability of the strain Bacillus thuringiensis var. subtoxicus to produce extracellular ribonuclease (ribonuclease Bt) was studied. It was found that the culture medium possesses a RNA-depolymerizing activity whose maximum is observed 4-5 hours after the beginning of the linear growth phase. A three-step chromatography of the culture extract on phosphocellulose resulted in a homogeneous enzyme with a molecular mass of 12000 Da. The enzyme showed the maximum activity towards RNA at pH 8.5, catalyzed the hydrolysis of polyribonucleotides and guanosine-2',3'-cyclophosphate. Hence, the enzyme can be related to base-nonspecific cyclizing ribonucleases showing the guanylic specificity towards nucleoside-2',3'-cyclophosphates.     

First demonstration of lactoribonuclease, a ribonuclease from bovine milk with similarity to bovine pancreatic ribonuclease

The isolation of a ribonuclease designated lactoribonuclease, with a molecular weight and an N-terminal amino acid sequence identical to those of bovine pancreatic ribonuclease, was first reported from bovine milk. After removal of globulin from acid whey by precipitation with 1.8 M (NH4)2SO4, (NH4)2SO4 was added to attain a concentration of 3.6 M. Adsorption on the ion exchanger CM-Sepharose and subsequently on Mono S by fast protein liquid chromatography yielded pure lactoribonuclease. The enzyme, like pancreatic ribonuclease, was most active at pH 7.5 with yeast transfer RNA (tRNA) as substrate. Lactoribonuclease and pancreatic ribonuclease showed a strong preference for poly(C) over poly(U). However, pancreatic ribonuclease did so with a higher specific activity, suggesting that the two ribonucleases are not identical. No inhibitory effect was shown by either lactoribonuclease or pancreatic ribonuclease toward poly (A) and poly (G). The effect of lactoribonuclease and pancreatic ribonuclease on tRNA increased with the concentration of tRNA. Lactoribonuclease inhibited cell-free translation in a rabbit reticulocyte lysate system with an IC50 of 3.5 nM while the corresponding IC50 for pancreatic ribonuclease was 0.09 nM.     

Enzymatic incorporation into oligonucleotides of modified nucleosides

Behaviour of modified nucleosides, tRNA components, and their analogues has been studied in the internucleotide bond formation catalysed by ribonucleases of various substrate specificity, polynucleotide phosphorylases, and T4 RNA ligase and the results are summarised in this paper. Pseudouridine, dihydrouridine, ribothymidine, 5-methylcytidine, inosine, and 6-methyladenosine can participate in the reaction of internucleotide bond formation the presence of most ribonucleases used, viz. Pb2, Pcl2, Pb1, Pch1, C2, T1, pancreatic RNase. 3-Methylcytidine and 4-acetylcytidine form internucleotide bond (as phosphate acceptors) usually by means of guanyl-specific ribonucleases, whereas 1-methylandenosine is incorporated with ribonuclease Pel2. 7-Methylguanosine and 1-methylguynosine 2',3'-cyclophosphates can be used as phosphate donors in the presence of ribonuclease Pb2; in the similar enzymatic reaction 6-isopentenyladenosine is an uneffective acceptor.     

Affinity chromatography of Nicotiana tabacum ribonucleases

The purification of tobacco ribonuclease by affinity chromatography is described. 5′-(4-amino-phenylphosphoryl)-guanosine 2′, (3′) phosphate, a ribonuelease inhibitor, has been synthesized and insolubilized onto agarose beads. The resulting adsorbent binds tobacco and some other plant ribonucleases strongly but reversibly at pH 5.4. The bound enzyme can be eluted by changing the pH or ionic strength of the eluting buffer, or by specific elution with substrate or inhibitor. Binding is not due to simple ion-exchange properties of the adsorbent.     

Isolation of a new ribonuclease from fruiting bodies of the silver plate mushroom Clitocybe maxima

A ribonuclease, with an N-terminal sequence exhibiting some homology to ribonuclease from Pleurotus ostreatus (Family Pleurotaceae), has been purified from fruiting bodies of the silver plate mushroom Clitocybe maxima (Family Tricholomataceae). However, there is little resemblance between the N-terminal sequences of ribonucleases from various Pleurotus species, and a lesser extent of resemblance between ribonucleases from C. maxima and Pleurotus tuber-regium. No structural relationship exists between ribonuclease from C. maxima, and those from Volvariella volvacea, Lentinus edodes and Irpex lacteus. The purification protocol involved ion exchange chromatography on DEAE-cellulose, affinity chromatography on Affi-gel blue gel, ion exchange chromatography on CM-Sepharose, and fast protein liquid chromatography on Superdex 75. The ribonuclease was unadsorbed on DEAE-cellulose and adsorbed on Affi-gel blue gel and CM-Sepharose. It exhibited a molecular mass of 17.5 kDa in both gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It manifested roughly the same ribonucleolytic potency toward poly A and poly G followed by poly U. Its activity toward poly C was, by comparison, meager. The temperature and pH required for its optimal activity were, respectively, 70 degrees C and 6.5-7.0.     

12 S small nuclear ribonucleoprotein-associated acidic-and pyrimidine-specific endoribonuclease from calf thymus and L5178y cells

12 S ribonucleoprotein (RNP) particles were separated from a 45 S RNP complex (Bachmann, M., Zahn, R. K. and Müller, W. E. G. (1983) J. Biol. Chem. 258, 7033-7040) isolated from calf thymus and L5178y cells. The particles were determined to be associated with an acidic endoribonuclease (pI 4.1; pH optimum 6.2). the enzyme requires Mg2+ and is sensitively inhibited by higher NaCl concentrations. The nuclease specifically degrades poly(U) and poly(C) in an endonucleolytic manner; the end-products are 3'-UMP (85%) and 2',3'-cyclic UMP (12%). Poly(A) strongly inhibits the pI 4.1 endoribonuclease activity. The Michaelis constant (for poly(U)) was determined as 82 microM and the maximal reaction velocity was 0.54 mumol/microgram per h. The endoribonuclease is distinguished from the known pyrimidine-specific ribonucleases (pancreatic ribonuclease and endoribonuclease VII) by further criteria, e.g., resistance to thiol reagents, inhibition by EDTA, Mg2+ requirement, pI and pH optimum. Using the techniques of counterimmunoelectrophoresis and immunoaffinity column chromatography it was shown that the pI 4.1 endoribonuclease-associated 12 S RNP particles display antigenicity to anti-Sm and anti-(U1)-RNP antibodies. An RNA component, isolated from the 12 S-45 S hypercomplex, was identified as U1-snRNA.     

Isolation and characterization of a human colon carcinoma-secreted enzyme with pancreatic ribonuclease-like activity

A ribonuclease was isolated from serum-free supernatants of the human colon adenocarcinoma cell line HT-29. It was purified by cation-exchange and C18 reversed-phase high-performance liquid chromatography. The protein is basic, has a molecular weight of approximately 16,000, and has an amino acid composition that is significantly different from that of human pancreatic ribonuclease. The amino terminus is blocked, and the carboxyl-terminal residue is glycine. The catalytic properties of this ribonuclease resemble those of the pancreatic ribonucleases in numerous respects. Thus, it exhibits a pH optimum of approximately 6 for dinucleotide cleavage and employs a two-step mechanism in which transphosphorylation to a cyclic 2',3'-phosphate is followed by slower hydrolysis to produce a 3'-phosphate. It does not cleave NpN' substrates in which adenosine or guanosine is at the N position and prefers purines at the N' position. Like bovine ribonuclease A, the HT-29-derived ribonuclease is inactivated by reductive methylation or by treatment with iodoacetate at pH 5.5 and is strongly inhibited by the human placental ribonuclease inhibitor. However, in contrast, the tumor enzyme does not cleave CpN bonds at an appreciable rate and prefers poly(uridylic acid) as substrate 1000-fold over poly(cytidylic acid). It also hydrolyzes cytidine cyclic 2',3'-phosphate at least 100 times more slowly than uridine cyclic 2',3'-phosphate and is inhibited much less strongly by cytidine 2'-monophosphate than by uridine 2'-monophosphate. Other ribonucleases known to prefer poly(uridylic acid) were isolated both from human serum and from liver and were compared with the tumor enzyme. The physical, functional, and chromatographic properties of the serum ribonuclease are essentially identical with those of the tumor enzyme. The liver enzymes, however, differ markedly from the HT-29 ribonuclease. The potential utility of the tumor ribonuclease in the diagnosis of cancer is considered.