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.     

Studies on extracellular ribonucleases of Ustilago sphaerogena. Purification and properties

1. Four ribonucleases were isolated from culture media of Ustilago sphaerogena. They were designated ribonucleases U(1), U(2), U(3) and U(4). 2. They were purified about 1600-, 3700-, 1100- and 16-fold respectively. 3. It was shown by gel filtration that ribonucleases U(1), U(2) and U(3) have molecular weights about 10000 like ribonuclease T(1), and that ribonuclease U(4) is much larger. 4. Ribonucleases U(1), U(2) and U(3) are thermostable, but ribonuclease U(4) is not. 5. The pH optimum of ribonucleases U(1) and U(4) is pH8.0-8.5, and that of ribonucleases U(2) and U(3) is pH4.5.     

3-Ribosyl-6-methyluracil as a phosphate acceptor in the synthesis of the internucleotide bond catalyzed by pancreatic ribonuclease.

The synthesis of uridylyl-(3'-5')-3-ribosyl-6-methyluracil (UprmU) catalyzed by pancreatic ribonuclease (EC 3.4.1.22) has been performed using uridine 2', 3'-cyclic phosphate (U greater than p) as phosphate donor and 3-ribosyl-6-methyluracil (rmU) as phosphate acceptor. The rate of synthesis of UprmU is much higher than that of uridylyl-(3'-5')-uridine (UpU) in a control experiment under the same conditions with uridine as acceptor. The yields of UpU and UprmU were 20 and 17% respectively. The competitive hydrolysis of the initial U greater than p also proceeds faster when rmU is used as the acceptor. The relationship between the conformation of this nucleoside and its acceptor activity in the enzymatic synthesis of the internucleotide bond is discussed.     

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 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 .     

cDNA structure and regulatory properties of a family of starvation-induced ribonucleases from tomato

In previous work we have determined the primary structure of two of the five ribonucleases which are induced by phosphate starvation in cultured tomato cells. Here, we present the isolation and characterization of the cDNAs for the extracellular ribonuclease LE and the intracellular, but extravacuolar ribonuclease LX. Structural analysis of these cDNAs together with partial protein-sequencing of vacuolar ribonucleases LV1, LV2 and LV3 revealed a family of very similar ribonucleases. From these data we assume identity between ribonucleases LE and LV3 for which the targeting mechanism has to be shown. Furthermore, RNase LV1 and RNase LV2 might be posttranslational processing products of RNase LX which travel to the vacuoles after splitting off the putative ER retention signal present at RNase LX. Additionally, we show by northern blot analysis that phosphate starvation in plant cells leads to an increase in the steady-state level of this type of enzymes revealing close similarities of the plant response to a limited supply of inorganic phosphate with the PHO regulation in bacteria and fungi.     

A novel endoribonuclease from the marine sponge Tethya aurantium specific to 2',5'-phosphodiester bonds

In the marine sponge Tethya aurantium a novel endoribonuclease was found which specifically catalyzed the degradation of 2′,5′-phosphodiester linkages and was therefore named endo-2′,5′-ribonuclease. This enzymatic reaction yielded 2′,3′-cyclic phosphate and 5′-OH products similarly to the 3′–5′ bond cleavage in RNA, catalyzed by metal-independent ribonucleases. The partially purified enzyme preparation was used for its biochemical characterization. The enzyme did not require the presence of metal ions for its activity. The novel nuclease exhibited a preference for 5′-phosphorylated 2′,5′-oligoadenylates, but 2′–5′ linkage in 5′-triphosphorylated hetero-oligomers or homo-dimers comprising guanylate or uridylate residues instead of adenylate was cleaved as well. The enzyme was also able to catalyze the degradation of 5′-unphosphorylated 2′,5′-oligoadenylates, except for 2′,5′-diadenylate, which were weaker substrates for the enzyme than the respective 5′-triphosphorylated forms. The observed substrate specificity may refer to the specific role of the enzyme in the degradation of natural 2′,5′-oligoadenylates (2-5A) that function in the interferon-induced mammalian 2-5A system as allosteric regulators of ribonuclease L. They are produced by 2-5A synthetases (OAS) that are also present in sponges, the most ancient phylum of Metazoa. We suggest that the newly discovered endoribonuclease found in the marine sponge T. aurantium could be a representative of the group of 2′,5′-specific ribonucleases that primarily control the cellular levels of 2′,5′-oligoadenylates.     

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.     

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.     

Enzymatic and NMR analysis of oligoribonucleotides synthesized with 2''-tert-butyldimethylsilyl protected cyanoethylphosphoramidite monomers.

The regioisomeric integrity of the internucleotide phosphate linkage in synthetic RNA using 2'-tert-butyldimethylsilyl protection was examined using enzymatic and NMR techniques. Two sets of DNA-RNA hybrid nonamers, T3XT5 and T5XT3 (where X = rA, rC, rG and U) and the tetramer AGCU were analyzed. Enzyme catalyzed hydrolysis of the nonamers with ribonuclease T2 showed that the linkage at the ribonucleotide was the desired 3'-5'. A control nonamer with a 2'-5' linkage was subjected to the enzyme, and showed no cleavage. High-resolution proton NMR of the tetramer also gave a favorable comparison with the same molecule obtained by non-chemical means.     

THE SYNTHESIS OF DITHYMIDINE BORANOPHOSPHATE BY THE OXATHIAPHOSPHOLANE APPROACH

The application of the oxathiaphospholane approach for the synthesis of dithymidine boranphospate was evaluated. It was shown, that although the nucleoside-3′-O-oxathiaphospholane-borane complexes 2 or 6 could not be chromatographically separated into diastereomerically pure species due to their apparent instability to moisture, they can be successfully applied to the non-stereocontrolled formation of internucleotide boranophosphate bond by reaction with 5′-OH-nucleoside in the presence of DBU. Attempts to apply the related dithiaphospholane approach for the preparation of dithymidine boranophosphorothioate were unsuccessful.     

Effect of nucleic-acid-binding compounds on the hydrolytic activity of various ribonucleases.

Studies were conducted on the stimulatory effect that various nucleic-acid-binding compounds have on the hydrolysis of RNA and polyribonucleotides by pancreatic ribonuclease A and by other ribonucleases. The stimulatory activity of chloroquine on tRNA hydrolysis by pancreatic ribonuclease was due to the formation of oligonucleotides of a wide range of sizes and was not due to the formation of very short ( n greater than 5) oligonucleotide fragments of tRNA. The dextrorotatory and levorotatory isomers of chloroquine did not differ in their ability to stimulate the hydrolysis of tRNA by pancreatic ribonuclease A. In addition to chloroquine and primaquine, other nucleic-acid-binding compounds (e.g., quinacrine, lucanthone, and proflavin) stimulated the hydrolysis of tRNA by pancreatic ribonuclease A. Chloroquine did not alter the rate of hydrolysis by pancreatic ribonuclease A of low-molecular-weight substrates (cytidine cyclic 2':o'-monophosphate, uridine cyclic 2':3'-monophosphate, cytidylyl-adenosine, or uridylyl-uridine). Furthermore, chloroquine and primaquine did not affect the hydrolysis of poly(A) by high concentrations of pancreatic ribonuclease A. In studies on the hydrolysis of tRNA by other endoribonucleases, several of the nucleic-acid-binding compounds (e.g., quinacrine and ethidium) exhibited appreciable inhibition of both ribonuclease N1 and ribonuclease T1. None of the compounds tested stimulated the activity of ribonuclease T1, and only chloroquine, and perhaps lucanthone, stimulated the hydrolysis of tRNA by ribonuclease N1.     

Interaction of the phage T4 Dam DNA-[N6-adenine] methyltransferase with oligonucleotides containing native or modified (defective) recognition sites.

The DNA-[N 6-adenine]-methyltransferase (Dam MTase) of phage T4 catalyzes methyl group transfer from S-adenosyl-l-methionine (AdoMet) to the N6-position of adenine in the palindromic sequence, GATC. We have used a gel shift assay to monitor complex formation between T4 Dam and various synthetic duplex oligonucleotides, either native or modified/defective. The results are summarized as follows. (i) T4 Dam bound with approximately 100-fold higher affinity to a 20mer specific (GATC-containing) duplex containing the canonical palindromic methylation sequence, GATC, than to a non-specific duplex containing another palindrome, GTAC. (ii) Compared with the unmethylated duplex, the hemimethylated 20mer specific duplex had a slightly increased ( approximately 2-fold) ability to form complexes with T4 Dam. (iii) No stable complex was formed with a synthetic 12mer specific (GATC-containing) duplex, although T4 Dam can methylate it. This indicates that there is no relation between formation of a catalytically competent 12mer-Dam complex and one stable to gel electrophoresis. (iv) Formation of a stable complex did not require that both strands be contiguous or completely complementary. Absence of a single internucleotide phosphate strongly reduced complex formation only when missing between the T and C residues. This suggests that if T4 Dam makes critical contact(s) with a backbone phosphate(s), then the one between T and C is the only likely candidate. Having only one half of the recognition site intact on one strand was sufficient for stable complex formation provided that the 5'G.C base-pairs be present at both ends of the palindromic, GATC. Since absence of either a G or C abolished T4 Dam binding, we conclude that both strands are recognized by T4 Dam.     

Laccase-catalyzed oxidation of 1-(3,4-dimethoxyphenyl)-1-propene using ABTS as mediator

The fungal laccases catalyzed oxidation of 1-(3,4-dimethoxyphenyl)-1-propene (2) with dioxygen in acetate buffer (pH 4.5) producing 1-(3,4-dimethoxyphenyl)propane-1,2-diol (4) and its 1-O-acetyl and 2-O-acetyl derivatives 5 and 6, and 3,4-dimethoxybenzaldehyde (7). However, in phosphate buffer (pH 5.9), the same reaction produced only 4 and 7. When 4 was treated in the same fashion in the phosphate buffer, it was converted into 7 with more than 95 mol% yield. This, together with the formation of 5 and 6 in the acetate buffer, showed that 2 is converted into 3–5 via 1-(3,4-dimethoxyphenyl)propane-1,2-epoxide (3) in the acetate buffer in the presence of ABTS. The major reaction of fungal laccase-catalyzed oxidation of 2 with dioxygen in the presence of ABTS is epoxidation of the double bond conjugated to the aromatic ring.     

The structure and function of ribonuclease T1. XX. Specific inactivation of ribonuclease T1 by reaction with tosylglycolate.

1. Ribonuclease T1 [EC 3.1.4.8] was inactivated by reaction with tosylglycolate (carboxymethyl rho-toluenesulfonate). At pH 5.5 and 8.0, alkylation of the gamma-carboxyl group of glutamic acid-58 appeared to be the predominant reaction and the major cause of inactivation by tosylglycolate, as in the case of the iodoacetate reaction, although the rate of inactivation was slower than that by iodoacetate. At pH 8.0, histidine residues were also alkylated to some extent. 2. The maximal rate of inactivation was observed at around pH 5.5 and the pH dependence of the rate of inactivation suggested the implication of two groups in the reaction, with apparent pKa values of about 3-4 (possibly histidine residue(s)). 3. In the presence of substrate analogs, ribonuclease T1 was markedly protected from inactivation by tosylglycolate at pH 5.5. The extent of protection corresponded to the binding strength of the substrate analog, except for guanosine. Ribonuclease T1 was much less protected from inactivation by guanosine than by 3'-AMP or 3'-CMP, which has a lower binding strength toward ribonuclease T1. This may indicate that glutamic acid-58 is situated in the catalytic site, at which the phosphate moiety of these nucleotides directly interacts. 4. Enzyme which had been extensively inactivated with tosylglycolate at pH 5.5 scarcely reacted with iodoacetate at pH 5.5, suggesting that these reagents react at the same site, i.e. glutamic acid-58. On the other hand, enzyme which had been inactivated almost completely with tosylglycolate at pH 8.0 still reacted with iodoacetate to some extent at pH 8.0, and the modes of reaction of tosylglycolate and iodoacetate toward ribonuclease T1 appeared to be somewhat different.     

Pulse sequences for detection of NH2···N hydrogen bonds in sheared G⋅A mismatches via remote, non-exchangeable protons

The non-detectability of NH...N hydrogen bonds in nucleic acids due to exchange broadened imino/amino protons has recently been addressed via the use of non-exchangeable protons for detecting internucleotide 2hJ(NN) couplings. In these applications, the appropriate non-exchangeable proton is separated by two bonds from the NH...N bond. In this paper, we extend the scope of this approach to protons which are separated by four bonds from the NH...N moiety. Specifically, we consider the case of the commonly occurring sheared G x A mismatch alignment, in which we use the adenine H2 proton to report on the (A)N6H6(1.2)...N3(G) hydrogen bond, in the presence of undetectable, exchange broadened N6H6(1.2) protons. Two sequences, the 'straight-through' (H6)N6N3H2 and 'out-and-back' H2N6N3 experiments, are presented for observing these correlations in H2O and D2O solution, respectively. The sequences are demonstrated on two uniformly 15N,13C labelled DNA samples: d(G1G2G3T4T5C6A7G8G9)2, containing a G3 x (C6-A7) triad involving a sheared G3 x A7 mismatch, and d(G1G2G3C4A5G6G7T8)4, containing an A5 x (G3 x G6 x G3 x G6) x A5 hexad involving a sheared G3 x A5 mismatch.     

Kinetic studies on turtle pancreatic ribonuclease: a comparative study of the base specificities of the B2 and P0 sites of bovine pancreatic ribonuclease A and turtle pancreatic ribonuclease

Kinetic constants for the transesterification of eight dinucleoside phosphates CpX and UpX by bovine and turtle pancreatic ribonuclease were determined. Both ribonucleases have a preference for purine nucleotides at the position X. However, bovine ribonuclease, like other mammalian ribonucleases, prefers 6-amino bases at this site, while turtle ribonuclease prefers 6-keto bases. This difference in specificity at the B2 site may be explained by the substitution of glutamic acid at position 111 by valine in turtle ribonuclease. These results have been confirmed by inhibition studies with the four nucleoside triphosphates. Inhibition studies with pT and pTp showed that a cationic binding group (P0) for the 5'-phosphate of the pyrimidine nucleotides bound at the primary B1 site is present in turtle ribonuclease, although lysine at position 66 in bovine ribonuclease is absent in turtle ribonuclease. However, the side chain of lysine 122 in turtle ribonuclease is probably located in the correct position to take over the role as cationic P0 site.     

Synthesis and Biological Activity of 3′-Modified 2′-5′ Adenylate Trimers

Abstract

One of the most important mediators in the mode of action of interferon is the (2′-5′)(A)n synthetase-RNase L pathway. The 2′-5′oligoadenylates (2–5A), synthesized from ATP, activate a pre-existing endonuclease that cleaves single-stranded RNA. The biological activity of 2–5A is rapidly lost due to cleavage of the 2′-5′ internucleotide bond by a specific 2′-5′-phosphodiesterase starting at the 3′end. This rapid cleavage and the poor uptake of 2–5A in intact cells limit the use of 2–5A as an antiviral or antineoplastic agent. Although several modified 2–5A analogues have been synthesized in order to improve the enzymatic stability, only few have proven to be resistant to degradation and still able to activate the 2–5A dependent endonuclease. 1-4 On the other hand, relative drastic methodology such as calcium coprecipitation, microinjection and liposome encapsulation5 has been used to introduce 2–5A into intact cells. Here, we present the synthesis and biological activity of oligoadenylates in which one or more adenosine residues were replaced by 9-(3-azido-3-deoxy-6-D-xylofuranosyl)adenine or 9-(3-amino-3-deoxy-D-xylofuranosyl)adenine. The oligonucleotides were synthesized by the phosphotriester method with triisopropylbenzenesulfonyl-chloride in the presence of N-methylimidazole as the condensing agent. The p-nitrophenylethyl group was used as the protecting group for the 2′-hydroxylfunction .(carbonate), the internucleotide linkage (phosphate ester) and the exocyclic amino groups of the heterocyclic base (carbamate). Bis(p-nitrophenylethy1)phosphoromonochloridate was used to phosphorylate the 5′-hy-droxyl group. All these blocking groups were removed with DBU in pyridine.     

Catalysis of the oxidative folding of ribonuclease A by protein disulfide isomerase: pre-steady-state kinetics and the utilization of the oxidizing equivalents of the isomerase

At low concentrations of a glutathione redox buffer, the protein disulfide isomerase (PDI) catalyzed oxidative renaturation of reduced ribonuclease A exhibits a rapid but incomplete activation of ribonuclease, which precedes the steady-state reaction. This behavior can be attributed to a GSSG-dependent partitioning of the substrate, reduced ribonuclease, between two classes of thiol/disulfide redox forms, those that can be converted to active ribonuclease at low concentrations of GSH and those that cannot. With catalytic concentrations of PDI and near stoichiometric concentrations of glutathione disulfide, approximately 4 equiv (2 equiv of ribonuclease disulfide) of GSH are formed very rapidly followed by a slower formation of GSH, which corresponds to an additional 2 disulfide bond equiv. The rapid formation of RNase disulfide bonds and the subsequent rearrangement of incorrect disulfide isomers to active RNase are both catalyzed by PDI. In the absence of GSSG or other oxidants, disulfide bond equivalents of PDI can be used to form disulfide bonds in RNase in a stoichiometric reaction. In the absence of a glutathione redox buffer, the rate of reduced ribonuclease regeneration increases markedly with increasing PDI concentrations below the equivalence point; however, PDI in excess over stoichiometric concentrations inhibits RNase regeneration.     

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.