Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.27.3 (RNase T1)
 1,228 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A method is described to classify, in regard to their location within the genome, fragments obtained by partial cleavage of 32P-labeled bacteriophage Qbeta RNA. The location of many fragments suitable for sequence analysis could be established using as markers 29 large RNase T1-resistant oligonucleotides with known map positions. Applying this method four fragments originating from the coat protein cistron were isolated and analyzed. The sequence of a segment of 239 nucleotides located immediately adjacent to the initiation triplet was determined to be G-C-A-A-A-A-U-U-A-G-A-G-A-C-U-G-U-U-A-C-U-U-U-A-G-G-U-A-A-C-A-U-C-G-G-G-A-A-A-G-A-U-G-G-A-A-A-A-C-A-A-A-C-U-C-U-G-G-U-C-C-U-C-A-A-U-C-C-G-C-G-U-G-G-G-G-U-A-A-A-U-C-C-C-A-C-U-A-A-C-G-G-C-G-U-U-G-C-C-U-C-G-C-U-U-U-C-A-C-A-A-G-C-G-G-G-U-G-C-A-G-U-U-C-C-U-G-C-G-C-U-G-G-A-G-A-A-G-C-G-U-G-U-U-A-C-C-G-U-U-U-C-G-G-U-A-U-C-U-C-A-G-C-C-U-U-C-U-C-G-C-A-A-U-C-G-U-A-A-G-A-A-C-U-A-C-A-A-G-G-U-C-C-A-G-G-U-U-A-A-G-A-U-C-C-A-G-A-A-C-C-C-G-A-C-C-G-C-U-U-G-C-A-C-U-G-C-A-A-A-C-G-G-U-U-C-U-U-Gp. The primary structure and the secondary structure model derived from it did not provide any evidence of homology with the corresponding RNA region of bacteriophage MS2.
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PMID:Determination of the first half of the coat protein cistron of bacteriophage Qbeta as an application of a mapping procedure for RNA fragments. 36 41

2-Thiocytidine 5'-triphosphate, s2CTP, is able to replace CTP as a substrate for tRNA nucleotidyltransferase. s2CMP can be incorporated into both cytidine sites of the C-C-A terminus common to all tRNAs, and in the absence of ATP into at least two additional positions. This was shown by alkylation of the 2-thiocytidine residues with iodo[14C]acetamide, total nucleoside analysis, microgel electrophoresis and analysis of RNase T1 fragments of these tRNAs. The incorporation of the 3'-terminal AMP is not influenced by the additional s2CMP residues at pH 9.0. However, at pH 7.6 the additional s2CMP residues are hydrolysed and AMP can be incorporated into the normal position. Two different tRNAs with terminal 2-thiocytidine alkylated by iodoacetamide inhibit tRNA nucleotidyltransferase. This inhibition is significantly slower if an elongated species is used compared to a tRNA with alkylated 2-thiocytidine in the normal position 75. The addition of 2-mercaptoethanol reactivates the enzyme and leads to a cytidine containing tRNA. This reaction identifies the attacking nucleophile of the enzyme as cysteine residue, which is probably identical to a cysteine residue found in a similar experiment reported previously. The mechanism of the enzymatic and chemical reactions is discussed.
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PMID:Reversible inactivation of tRNA nucleotidyltransferase from baker's yeast by tRNAPhe containing iodoacetamide-alkylated 2-thiocytidine in normal and additional positions. 37 62

The topography and the length of the non-ribosomal sequences present in 7-S RNA, the immediate precursor of 5.8-S ribosomal RNA, from the yeast Saccharomyces carlsbergensis were determined by analyzing the nucleotide sequences of the products obtained after complete digestion of 7-S RNA with RNase T1. The results show that 7-S RNA contains approximately 150 non-ribosomal nucleotides. The majority (90%) of the 7-S RNA molecules was found to have the same 5'-terminal pentadecanucleotide sequence as mature 5.8-S rRNA. The remaining 10% exhibited 5'-terminal sequences identical to those of 5.9-S RNA, which has the same primary structure as 5.8-S rRNA except for a slight extension at the 5' end [Rubin, G.M. (1974) Eur. J. Biochem. 41, 197--202]. These data show that the non-ribosomal nucleotides present in 7-S RNA are all located 3'-distal to the mature 5.8-S rRNA sequence. Moreover, it can be concluded that 5.9-S RNA is a stable rRNA rather than a precursor of 5.8-S rRNA. The 3'-terminal sequence of 5.8-S rRNA (U-C-A-U-U-UOH) is recovered in a much longer oligonucleotide in the T1 RNase digest of 7-S RNA having the sequence U-C-A-U-U-U-(C-C-U-U-C-U-C)-A-A-A-C-A-(U-U-C-U)-Gp. The sequences enclosed in brackets are likely to be correct but could not be established with absolute certainty. The arrow indicates the bond cleaved during processing. The octanucleotide sequence -A-A-A-C-A-U-U-C- located near the cleavage site shows a remarkable similarity to the 5'-terminal octanucleotide sequence of 7-S RNA (-A-A-A-C-U-U-U-C-). We suggest that these sequences may be involved in determining the specificity of the cleavages resulting in the formation of the two termini of 5.8-S rRNA.
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PMID:Non-ribosomal nucleotide sequences in 7-S RNA, the immediate precursor of 5.8-S ribosomal RNA in yeast. 41 62

Previous genetic and biochemical studies led to the identification of two large RNase T1-resistant oligonucleotides, designated the G(IX) (+) and G(IX) (-) oligonucleotides, whose presence in the genomes of closely related murine leukemia viruses is mutually exclusive and predictive of two properties of the viral envelope glycoprotein gp70. Viruses harboring the G(IX) (+) oligonucleotide induce expression of the gp70-associated antigen G(IX) and possess gp70s with more rapid electrophoretic mobility on sodium dodecyl sulfate/polyacrylamide gels than viruses that possess the G(IX) (-) oligonucleotide. The latter viruses fail to induce G(IX) on infected fibroblasts. The G(IX) (+) and G(IX) (-) oligonucleotides lie in corresponding positions in the 3' third of the oligonucleotide maps of their respective viruses. We have determined the nucleotide sequences of the G(IX) (+) and G(IX) (-) oligonucleotides. The sequence of the G(IX) (-) oligonucleotide is U-A-U-C-U-C-A-A-C-C-A-C-C-A-U-A-C-U-U-A-A-C-C-U-C-A-C-C-A-C-[unk]-G, and the sequence of the G(IX) (+) oligonucleotide is U-A-U-C-U-C-A-A-C-C-A-C-C-A-U-A-C-U-U-G. Thus, a single base change could result in the interconversion of the two oligonucleotides. Consideration of the amino acids specified by the two oligonucleotides suggests that this single base difference may result in the presence of an additional oligosaccharide chain in the gp70s of the G(IX) (-) viruses. Evidence supporting this prediction has been obtained by M. R. Rosner, J.-S. Tung, E. Fleissner, and P. W. Robbins (personal communication). It is entirely possible that the single nucleotide change that apparently results in a different electrophoretic mobility of the gp70s of the G(IX) (+) and G(IX) (-) viruses is also responsible for the presence or absence of the G(IX) antigenic determinant; however, the validity of this possibility awaits further investigation.
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PMID:Nucleotide sequences associated with differences in electrophoretic mobility of envelope glycoprotein gp70 and with GIX antigen phenotype of certain murine leukemia viruses. 615 37

N-Acetylvalyl-tRNA1Val (AcVal-tRNA1Val) was bound to the P site of uniformly 32P-labeled 70S ribosomes from Escherichia coli and crosslinked to 16S RNA in the 30S ribosomal subunit by irradiation with light of 300-400 nm. To identify the crosslinked nucleotide in 16S RNA. AcVal-tRNA1Val-16S [32P]RNA was digested completely with RNase T1 and the band containing the covalently attached oligonucleotides from tRNA and rRNA was isolated by polyacrylamide gel electrophoresis. The crosslinked oligonucleotide, and the 32P-labeled rRNA moiety released from it by photoreversal of the crosslink at 254 nm, were then analyzed by secondary hydrolysis with pancreatic RNase A and RNase U2. The oligonucleotide derived from 16S RNA was found to be the evolutionarily conserved sequence, U-A-C-A-C-A-C-C-G1401, and the nucleotide crosslinked to tRNA1Val, C1400. The identity of the covalently attached residue in the tRNA was established by using AcVal-tRNA1Val-16S RNA prepared from unlabeled ribosomes. This complex was digested to completion with RNase T1 and the resulting RNA fragments were labeled at the 3' end with [5'-32P]pCp. The crosslinked T1 oligonucleotide isolated from the mixture yielded one major end-labeled component upon photoreversal. Chemical sequence analysis demonstrated that this product was derived from the anticodon-containing pentadecanucleotide of tRNA1Val, C-A-C-C-U-C-C-C-U-cmo5U-A-C-m6A-A-G39(cmo5U, 5-carboxymethoxyuridine). A similar study of the crosslinked oligonucleotide revealed that the residue covalently bound to 16S was cmo5U34, the 5' or wobble base of the anticodon. The adduct is believed to result from formation of a cyclobutane dimer between cmo5U34 of tRNA1Val and C1400 of the 16S RNA.
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PMID:Covalent crosslinking of tRNA1Val to 16S RNA at the ribosomal P site: identification of crosslinked residues. 681 60

Pseudouridine, an isomer of uridine, is probably the most common of many posttranscriptional RNA modifications found in nature. Although mass spectrometry has become widely used in the characterization of modified nucleic acids, its application to the recognition and sequence placement of pseudouridine has not been straightforward, particularly in the case of complex mixtures such as those resulting from selective enzymatic hydrolysis of RNA into oligonucleotides. We report results of a study of the characteristic dissociation reactions of pseudouridine-containing oligonucleotides following ionization by electrospray and use of those pathways in an LC/MS-based method applicable to direct analysis of RNase digests of RNA. As a consequence of the C-C (rather than C-N) glycosidic bond of pseudouridine, the otherwise common dissociation paths involving base loss do not occur, resulting in characteristic formation of a set of low-mass negative ions containing the intact glycosidic bond (m/z 225, 207, 189, 165, 164, 139), which permit recognition of pseudouridine-containing oligonucleotides. Those components can subsequently be subjected to sequence analysis by MS/MS, in which enhancement of selective sequence-determining ions (a-, w-, y-types), and absence of a - base ions, are observed at the site of pseudouridylation. Also, selected reaction pathways can be monitored in the LC/MS/MS analysis that are indicative of pseudouridine at the 5' terminus (m/z 225 --> 165), internal positions (m/z 207 --> 164), and in the RNase T1-derived product Psi pGp (m/z 668 --> 207) arising from the RNA sequence ...G Psi G... These procedures can be effectively integrated into an existing suite of LC/ESI-MS-based methods designed for the analysis of posttranscriptionally modified sites in RNA.
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PMID:Detection of the common RNA nucleoside pseudouridine in mixtures of oligonucleotides by mass spectrometry. 1605 77