RNase U2 Research Articles

Ribonuclease U2: cloning, production in Pichia pastoris and affinity chromatography purification of the active recombinant protein.

RNase U2 is an endoribonuclease secreted by the fungus Ustilago sphaerogena. Its genomic DNA (rnu2), containing an intron of 116 bp, has been isolated and cloned. The corresponding cDNA has also been synthesized. The recombinant RNase U2 was successfully produced in Pichia pastoris, fused to the yeast alkaline phosphatase signal peptide. The recombinant RNase U2, purified by affinity chromatography, contains three extra amino acids at its amino-terminal end and retains the enzymatic and spectroscopic properties of the natural fungal protein.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) of endonuclease digests of RNA.

The determination of RNA sequences using base- specific enzymatic cleavages is a well established method. Different synthetic RNA molecules were analyzed for uniformity of degradation by RNase T1, U2, A and PhyM under reaction conditions compatible with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS), to identify the positions of G, A and pyrimidine residues. In order to get a complete set of fragments derived from cleavage at every phosphodiester bond, the samples were also subjected to a limited alkaline hydrolysis. Additionally, the 5'-terminus fragments of a 49mer RNA transcript were isolated by way of 5'-biotinylation and streptavidin-coated magnetic beads (Dynal), followed by a RNase U2digestion. MALDI-MS of the generated fragments is presented as an efficient technique for a direct read out of the nucleotide sequence.

A New Class of Pentacoordinate Ribonuclease Inhibitors: Synthesis, Characterization, and Inhibition Studies of Ribonucleoside and Anhydropentofuranose Oxorhenium(V) Complexes

This article describes the synthesis, characterization, and kinetic studies of a new class of stable ribonuclease (RNase) inhibitors. Herein the first synthesis of oxorhenium(V) complexes of diaminonucleosides and diaminoaldopentofuranoses is reported. Stability studies have shown that the complexes are stable between pH 3 and 13 at temperatures of 25−80 °C for 24 h with no occurrence of ligand exchange or epimerization at the ReO core. Kinetic studies show that both the syn (1a) and anti (1b) diastereoisomers of oxorhenium(V) complexes of 9-(2‘,3‘-diamino-2‘,3‘-dideoxy-β-d-ribofuranosyl)adenine (13) are excellent inhibitors of the purine specific ribonuclease, RNase U2. Dixon and Lineweaver−Burke analyses suggest that the inhibition is competitive, with inhibitory constants (Kis) of 15 and 93 μM, respectively. These complexes are of equivalent inhibitory potency to previously reported nucleoside vanadium alkoxide inhibitors with the added advantage of being completely stable in aqueous solution. The oxor...

Crystal Structure of Ustilago sphaerogena Ribonuclease U2 at 1.8 .ANG. Resolution

The crystal structure of purine-specific ribonuclease (RNase) U2 from Ustilago sphaerogena has been solved by the molecular replacement methods using RNase T1 as a search model. The structure, with 114 amino acid residues, 141 water molecules, and a sulfate ion, is refined to an R factor of 0.143 at 1.8 A resolution. As evidenced by the electron densities, residues 49 and 50 are revised to Glu 49 and Asp 50, respectively, and also Asp 45 is identified as a beta-isomerized form to L-isoaspartate with a beta-peptide linkage. RNase U2 consists of a beta-hairpin at residues from 7 to 14, a 4.4-turn alpha-helix from 16 to 32, a central beta-sheet with five strands, and a protruding beta-turn from 74 to 77. As for the catalytic site residues, His 41, Glu 62, and Arg 85 are located as constituents of the central beta-sheet, and Tyr 39 and His 101 are situated at either end of the beta-sheet. The side chains of Tyr 39, Glu 62, Arg 85, and His 101 are hydrogen-bonded to the sulfate ion which marks the RNA phosphate position. Though the side chain of His 41 is pointing away from the sulfate, small conformational adjustments of His 41 enable the side chain to interact with either the phosphate or the ribose group of RNA. The loop region from Tyr 44 to Asp 50 is ascribed to the base recognition site where Glu 49 is involved in adenine recognition. beta-Isomerized Asp 45 suggests that this region is conformationally flexible and alterable.

Revised sequence of ribonuclease U2 in the substrate-binding region.

Revised sequence of ribonuclease U2 in the substrate-binding region.

Distribution of Cross-links between mRNA Analogues and 16 S rRNA in Escherichia coli 70 S Ribosomes Made under Equilibrium Conditions and Their Response to tRNA Binding

The interaction between mRNA and Escherichia coli ribosomes has been studied by photochemical cross-linking using mRNA analogues that contain 4-thiouridine (s4U) or s4U modified with azidophenylacyl bromide (APAB), either two nucleotides upstream or eight nucleotides downstream from the nucleotide sequence ACC, the codon for tRNA(Thr). The sequences of the mRNA analogues were described earlier (Stade, K., Rinke-Appel, J., and Brimacombe, R. (1989) Nucleic Acids Res. 17, 9889-9908; Rinke-Appel, J., Stade, K., and Brimacombe, R. (1991) EMBO J. 10, 2195-2202). Under equilibrium conditions, both of these mRNA analogues bind and cross-link to 70 S ribosomes without the presence of tRNA(Thr); however, there are significant increases both in binding and particularly in cross-linking in the presence of the tRNA(Thr). Four regions contain cross-linking sites that increase in the presence of tRNA, C1395, A532, A1196 (and minor sites around these three positions), and C1533/U1532. Three other cross-linking sites, U723, A845, and U1381, show very little change in extent of cross-linking when tRNA is present. A conformational change in the 30 S subunit allowing additional accessibility to the 16 S rRNA by the mRNA analogues upon tRNA binding best explains the behavior of the tRNA-dependent and tRNA-independent mRNA-16 S rRNA cross-linking sites.

Capillary enzymophoresis of nucleic acid fragments using coupled capillary electrophoresis and capillary enzyme microreactors having surface-immobilized RNA-modifying enzymes.

This report describes the coupling of capillary enzyme reactors to capillary electrophoresis, which is termed capillary enzymophoresis. In the present study, the capillary enzyme reactors were prepared by immobilizing RNA-modifying enzymes, e.g., RNAse T1 and RNAse U2, on the inner walls of 50 microns fused-silica capillaries. These microreactors served to selectively modify the solutes (or substrates) before entering the separation capillary. Capillary enzymophoresis using single or mixed enzyme reactors proved useful in identifying minute amounts of dinucleotides as well as the fingerprinting of tRNAs. The immobilized RNase T1 and RNase U2 displayed their usual enzymic activities toward RNA fragments and in addition exhibited different activity-pH dependency than the soluble enzymes. This was attributed to microenvironmental effects arising from the charged nature of the capillary walls in the close proximity of the immobilized enzymes. The enzyme reactors were reusable for several RNA samples and showed chemical and thermal stability.

Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase.

Double-stranded RNA adenosine deaminase (dsRAD), previously called the double-stranded RNA (dsRNA) unwinding/modifying activity, modifies adenosines to inosines within dsRNA. We used ribonuclease U2 and a mutant of ribonuclease T1 to map the sites of modification in several RNA duplexes. We found that dsRAD had a 5' neighbor preference (A = U > C > G) but no apparent 3' neighbor preference. Further, the proximity of the strand termini affected whether an adenosine was modified. Most importantly, dsRAD exhibited selectivity, modifying a minimal number of adenosines in short dsRNAs. Our results suggest that the specific editing of glutamate receptor subunit B mRNA could be performed in vivo by dsRAD without the aid of specificity factors, and support the hypothesis that dsRAD is responsible for hypermutations in certain RNA viruses.

Purification and primary structure of a new guanylic acid specific ribonuclease from Pleurotus ostreatus.

A guanine nucleotide-specific RNase (RNase Po1) was isolated from caps of the fruit bodies of Pleurotus ostreatus. RNase Po1 is most active towards RNA at pH 8.0. The effect of heating on the molar ellipticity at 210 nm of RNase Po1 showed that RNase Po1 is more stable than RNase T1. The primary structure of RNase Po1 was determined to be < ETGVRSCNCAGRSFTGTDVTNAIRSARAGGSGNYPHVYNNFEGFSFSCTPTFFEFPVFRGSVYSGGSPG ADRVIYD- QSGRFCACLTHTGAPSTNGFVECRF. It consisted of 101 amino acid residues, with a molecular weight of 10,760. RNase Po1 has relatively higher sequence homology with RNase T1 family RNase. It contains 6 half cystine residues. The locations of four of them are superimposable on those of RNase U1 and RNase U2. The amino acid residues forming the active site of RNase T1 were well conserved in this RNase. Therefore, RNase Po1 is a unique member of the RNase T1 family in respect of the location of one disulfide bridge, and its stability.

Effects of amino-terminal extensions and specific mutations on the activity of restrictocin.

The cytotoxic activities of restrictocin with aminoterminal extensions and specific mutations were investigated using in vivo and in vitro systems. Genes were constructed from the cDNA clone of restrictocin which encode: the native form of restrictocin (including the leader sequence); Met-prorestrictocin, in which a codon for methionine was placed before a putative pro region; Met-mature restrictocin, with a methionine codon prior to the mature form of restrictocin; and three mutated forms of Met-mature restrictocin, E95G, E115G/H136L, and H136L. These constructions were placed under the control of the GAL1 promoter and were transformed into Saccharomyces cerevisiae. Transformants were killed, and a new RNA band formed when any of these genes except those containing the H136L mutation were expressed. Restrictocin protein was detected by immunoblot only in cells expressing the native form of restrictocin and the forms containing the H136L mutation. Native restrictocin, Met-prorestrictocin, and Met-mature restrictocin mRNA were translated in an in vitro system resulting in proteins of the expected molecular weight and inactivation of the translation system. Restrictocin was not inactivated by the presence of the leader sequence and the putative prosequence. Amino acid His136 is putatively in the active site of restrictocin by analogy to ribonuclease U2 and the elimination of toxic effects in the S. cerevisiae expression and in vitro translation systems.

Poly(A) binding proteins located at the inner surface of resealed nuclear envelopes.

We have used a photoreactive cross-linking reagent, poly(A/8-N3-A) (a poly(A) of average molecular mass of 100 kDa in which 5-10% of the A residues are replaced by 8-N3-A), to label poly(A) binding proteins of rat liver nuclear envelopes. This reagent was prepared by polymerizing a mixture of ADP and 8-N3-ADP with polynucleotide phosphorylase. The purified poly(A) was labeled in the 5'-position with a 32P group. In nuclear envelopes prepared by a low salt DNase I procedure, the poly(A/8-N3-A) labeled a protein-nucleic acid complex of approximately 270 kDa, which on degradation with RNase U2 or NaOH at pH 10 yielded two polypeptides of approximately 50 and 30 kDa. These photoreaction products were markedly decreased when resealed nuclear envelopes or non-nuclear envelope proteins were irradiated in the presence of poly(A/8-N3-A). The affinity labeling was intensified when resealed vesicles were made leaky by freezing or ultrasonication, suggesting that the poly(A) binding proteins are accessible from the nucleoplasmic but not the cytoplasmic face of the envelope. Moreover binding was specific for poly(A). Alternative reagents, random poly(A/8-N3-A,C,G,U) of about 100 kDa and poly(dA) (molecular mass between 350 and 515 kDa), showed a very low affinity for poly(A) recognition proteins in the low salt DNase I-treated nuclear envelopes; the 270-kDa band was labeled only weakly. The binding site was not protected by poly(A,C,G,U), weakly by poly(dA), and distinctly by poly(A).

Expression of the rat interferon- α1 gene in Escherichia coli controlled by the secondary structure of the translation-initiation region

A synthetic ribosome-binding site (RBS) containing a 7-nucleotide-long Shine-Dalgarno (SD) sequence was placed ahead of the rat interferon (IFN)- α 1 coding region. The translational efficiency of this construct was extremely low. Structural probing of transcripts with RNases T1 and U2 combined with computer predictions revealed the presence of a stable hairpin in which the SD region was base-paired to codons 3, 4 and 5 of the IFN mRNA. Each mutation in this stem changing an A-U to an A · C or a G-C a G · U pair increased translational efficiency about fourfold and this effect could be reversed by a compensating stabilizing substitution in the other strand of the stem. We conclude that the strength of an RBS is to a major degree determined by its involvement in secondary structure. We also show that the negative effect of secondary structure on the efficiency of an RBS can be overcome by allowing upstream translation to terminate within the base-paired region. In our clones, termination-dependent restarts occur at a frequency comparable to that taking place in constructs containing destabilized hairpins.

Capped poly(A) leaders of variable lengths at the 5' ends of vaccinia virus late mRNAs

Evidence for capped poly(A) leaders of variable lengths located immediately upstream of the translation initiation codon was obtained by direct analyses of a major late mRNA species. A decapping-recapping method was used to specifically substitute a radioactively labeled phosphate for an unlabeled one within the cap structure. RNase H-susceptible sites were made by hybridizing synthetic oligodeoxyribonucleotides to the mRNA encoding a late major structural protein of 11 kilodaltons. Sequences of the type m7G(5')pppAmp (Ap)nUpG. . ., where n varies from a few to more than 40 nucleotides, were deduced by analysis of the length and sequence of RNase H, RNase T1, and RNase U2 digestion products.

The amino acid sequence of ribonuclease U1, a guanine-specific ribonuclease from the fungus Ustilago sphaerogena.

The complete amino acid sequence of ribonuclease U1 (RNase U1), a guanine-specific ribonuclease from a fungus, Ustilago sphaerogena, was determined by conventional protein sequencing, using peptide fragments obtained by several enzymatic cleavages of the performic acid-oxidized protein. The oxidized protein was first cleaved by trypsin and the resulting peptides were purified and their amino acid sequences were determined. These tryptic peptides were aligned with the aid of overlapping peptides isolated from a chymotryptic digest of the oxidized protein. The amino acid sequence thus deduced was further confirmed by isolation and analysis of peptides obtained by digestion of the oxidized protein with lysyl endopeptidase. The location of the disulfide bonds was deduced by isolation and analysis of cystine-containing peptides from a chymotryptic digest of heat-denatured RNase U1. These results showed that the protein is composed of a single polypeptide chain of 105 amino acid residues cross-linked by two disulfide bonds, having a molecular weight of 11,235, and that the NH2-terminus is blocked by a pyroglutamate residue. It has an overall homology with other guanine-specific or related ribonucleases, and shows 48% identity with RNase T1 and 38% identity with RNase U2.

Analysis of tcRNA102 associated with myosin heavy chain-mRNPs in control and dystrophic chick pectoralis muscle.

Translational control RNA (tcRNA102) is closely associated with nonpolysomal myosin heavy chain-mRNA in mRNP particles. The nucleotide sequence of tcRNA102 has revealed a heterogeneity at the 3' end. This heterogeneity is mostly with regard to an ambiguity between adenine and guanine residues. tcRNA102 (obtained from pectoralis muscle) runs as a single band on denaturing acrylamide gels. When this band is extracted and rerun on a native gel at low voltage, two individual bands appear (A the slower moving and B the faster moving). From the partial RNase U2 sequence analysis and our previous sequence determinations (McCarthy, T. L., Siegel, E., Mrockowski, B., and Heywood, S. M. (1983) Biochemistry 22, 935-941), we may now assign tcRNA102 (A) the 3'-terminal sequence ... GGUUGGACGG-3' and tcRNA102(B) and 3' terminal sequence ... GAUUAAGCAA-3'. Analysis of the tcRNA102s indicates that dystrophic pectoralis muscle contains much less tcRNA102 than a similar preparation from control muscle. The tcRNA102 found in dystrophic pectoralis muscle is of the "A" type while normal pectoralis muscle contains predominantly the "B" type. In addition, control leg muscle from dystrophic chick contains predominantly "B" type. These results suggest that the differences observed at the DNA level (see accompanying paper, Zezza, D. J., and Heywood, S. M. (1986) J. Biol. Chem. 261, 7455-7460) may be reflected in the RNA transcripts.

Infectivity of Artificially Nicked Viroid Molecules

SUMMARY Circular molecules of potato spindle tuber viroid (PSTV) were subjected to limited digestion by various methods to produce nicked molecules. The resulting linear molecules were separated electrophoretically from circular ones, and assayed for infectivity. The linear molecules produced by treatment with RNase CI or RNase U2 were as infective as circular molecules. These linear molecules had 5′-OH and 3′-phosphate ends; almost all 3′ termini probably were in the form of 2′,3′-cyclic phosphate. However, the linear molecules produced by treatment with RNase T1 were approximately 10-fold less infective than circular molecules. The 2′,3′-cyclic phosphate at the 3′ end of these linear molecules had presumably been partially converted to 3′-phosphate. Linear molecules produced by a Mg2+-catalysed nicking reaction had a mixture of 2′- and 3′-terminal phosphates at their 3′ end and were approximately 100-fold less infective than circular ones. The infectivity of linear molecules produced by nuclease S1 digestion which lacked a 3′-phosphate was 100- to 1000-fold less than that of circular ones. These results indicate that the 3′-terminal phosphate of linear PSTV molecules is required for infectivity, and for maximum infectivity is required to be in the form of 2′,3′-cyclic phosphate.

Primary structure of a minor ribonuclease from Aspergillus saitoi.

1. RNase Ms, a base non-specific RNase from Aspergillus saitoi was reduced and carboxymethylated (RCM-RNase Ms). RCM-RNase Ms was hydrolyzed with trypsin, and the trypsin digests were then treated with chymotrypsin. Trypsin digests were also treated with Staphylococcus protease and with chymotrypsin, separately. 2. By the analyses of the amino acid sequences of the peptides formed, the alignment of these peptides in RCM-RNase Ms was determined. 3. From the digest of heat-denatured RNase Ms with Bacillus subtilis protease, two peptides containing disulfide bridges were isolated. From the analysis of these two peptides, the locations of the bridges were determined. 4. The amino acid sequence of RNase Ms was compared with those of RNase T1 (Asp. oryzae, guanine specific), RNase U1 (Ustilago sphaerogena, guanine specific) and RNase U2 (Ustilago sphaerogena, purine specific). There are very similar sequences between these for RNases irrespective of their differences in base specificity. These were, in RNase Ms, tripeptide sequence containing His39 (Tyr-Pro-His), the tetrapeptide containing Glu57 (Glu-Tyr-Pro-Ile), the hexapeptide containing Arg76 (Asp-Arg-Val-Ile-Phe-Asp) and the hexapeptide containing His 91 (Ile-Thr-His-Thr-Gly-Ala). The other sequences common for all four RNases are Tyr67, Phe100, and Cys103 in RNase Ms. Since among these peptides His39, Glu57, His91, and Arg76 in RNase Ms corresponded to His40, Glu58, His92, and Arg77 in RNase T1 which are known to be involved in the active site of RNase T1, the possible role of these amino acids in the active site of RNase Ms is discussed. 5. The sequence similarity of RNase Ms to that of RNase T1 was about 60% and to those of RNase U1 and RNase U2 was about 30%. 6. The details of the experimental evidence used to elucidate the amino acid sequence of RNase Ms are described in the supplemental miniprint.

Studies of catalysis by ribonuclease U2. Steady-state kinetics for transphosphorylation of oligonucleotide and synthetic substrates.

The values of the steady-state kinetic parameters for the RNase, U2 catalyzed transphosphorylation were measured for several di- and trinucleotides such as ApXp (X = A, C, G, or U), ApYpGp, and YpApGp (Y = C or U). The pH dependence of kcat/Km for ApUp indicated a dependence for catalysis upon an unprotonated group with pK = 3.8 and two proton-associated groups with pK = 4.4 and 5.0. As judged from kcat/Km values, ApUpGp and ApCpGp are better substrates than the corresponding parent dimers, ApUp and ApCp, respectively. By contrast, the kcat/Km for UpApGp was about 1/20 relative to that of the parent dimer, ApGp. The results were compared for possible thermodynamic and structural information about the chemical consequences. The inhibition of the RNase U2 catalyzed reaction of ApUp by a series of nucleosides and nucleotides was also studied. Evidence for similarities and dissimilarities in the binding and catalysis by RNase U2 and RNase T1 is presented.

An affinity adsorbent, 5'-adenylate-aminohexyl-sepharose. I. Purification and properties of two forms of RNase U2.

An affinity adsorbent, 5'-adenylate-aminohexyl-Sepharose 4B, was prepared by the periodate oxidation of AMp followed by coupling and condensation with amino-hexyl-Sepharose 4B. RNase U2, a purine-specific RNase, was specifically bound to this adsorbent at pH 4.5 and eluted critically at pH 5.9 in the presence of 1 M NaCl, corresponding to the pH dependence of the binding of 2'-AMP to RNase U2. By using this affinity chromatography as a main tool, a simplified and effective purification method for RNase U2 was established with a high yield of 58%. Another form of RNase U2 with low specific activity, named RNase U2-B, was eluted at a slightly higher pH from this adsorbent. RNase U2-B was indistinguishable from the original enzyme (RNase U2-A) in base specificity, affinity for ApA, molecular weight and amino acid composition, but was clearly different in specific activity, molecular activity for ApA, isoelectric point and conformation of molecule. This affinity adsorbent is also effective for the detection or isolation of small amounts of base-specific RNases in crude cell extract.

Specific interaction of base-specific nucleases with nucleosides and nucleotides.

Twentytwo years and eleven years, respectively, have passed since we discovered RNases T1 (Sato and Egami 1957) and U2 (Arima et al. 1968). Both enzymes are now quite familiar, described in most textbooks of biochemistry together with RNase A as important tools for the structural analysis of RNA. This is because of their base specificity: RNase A is, as is well known, specific for pyrimidine nucleotides and, on the contrary, RNase U2 is specific for purine nucleotides. RNase T1 is the most specific, namely it is specific for guanylate.