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Novel ribonuclease activity of cusativin from Cucumis sativus for mapping nucleoside modifications in RNA. Anal Bioanal Chem 2017; 409:5645-5654. [PMID: 28730304 DOI: 10.1007/s00216-017-0500-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/14/2017] [Accepted: 06/27/2017] [Indexed: 01/05/2023]
Abstract
A recombinant ribonuclease, cusativin, was characterized for its cytidine-specific cleavage ability of RNA to map chemical modifications. Following purification of native cusativin protein as described before (Rojo et al. Planta 194:328, 17), partial amino acid sequencing was carried out to identify the corresponding protein coding gene in cucumber genome. Cloning and heterologous expression of the identified gene in Escherichia coli resulted in successful production of active protein as a C-terminal His-tag fusion protein. The ribonuclease activity and cleavage specificity of the fusion protein were confirmed with a variety of tRNA isoacceptors and total tRNA. Characterization of cusativin digestion products by ion-pairing reverse-phase liquid chromatography coupled with mass spectrometry (IP-RP-LC-MS) analysis revealed cleavage of CpA, CpG, and CpU phosphodiester bonds at the 3'-terminus of cytidine under optimal digestion conditions. Ribose methylation or acetylation of cytosine inhibited RNA cleavage. The CpC phosphodiester bond was also resistant to cusativin-mediated RNA cleavage; a feature to our knowledge has not been reported for other nucleobase-specific ribonucleases. Here, we demonstrate the analytical utility of such a novel feature for obtaining high-sequence coverage and accurate mapping of modified residues in substrate RNAs. Graphical abstract Cytidine-specific novel ribonuclease activity of cusativin.
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2
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Daou-Chabo R, Condon C. RNase J1 endonuclease activity as a probe of RNA secondary structure. RNA (NEW YORK, N.Y.) 2009; 15:1417-25. [PMID: 19458035 PMCID: PMC2704070 DOI: 10.1261/rna.1574309] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 04/16/2009] [Indexed: 05/27/2023]
Abstract
Reliable determination of RNA secondary structure depends on both computer algorithms and experimental probing of nucleotides in single- or double-stranded conformation. Here we describe the exploitation of the endonucleolytic activity of the Bacillus subtilis enzyme RNase J1 as a probe of RNA structure. RNase J1 cleaves in single-stranded regions and, in vitro at least, the enzyme has relatively relaxed nucleotide specificity. We confirmed the feasibility of the approach on an RNA of known structure, B. subtilis tRNA(Thr). We then used RNase J1 to solve the secondary structure of the 5' end of the hbs mRNA. Finally, we showed that RNase J1 can also be used in footprinting experiments by probing the interaction between the 30S ribosomal subunit and the Shine-Dalgarno element of the hbs mRNA.
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Affiliation(s)
- Roula Daou-Chabo
- Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique UPR 9073, Université de Paris 7-Denis Diderot, 75005 Paris, France
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3
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Nygård O, Alkemar G, Larsson SL. Analysis of the secondary structure of expansion segment 39 in ribosomes from fungi, plants and mammals. J Mol Biol 2006; 357:904-16. [PMID: 16473366 DOI: 10.1016/j.jmb.2006.01.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2005] [Revised: 01/02/2006] [Accepted: 01/09/2006] [Indexed: 11/25/2022]
Abstract
The structure of expansion segment 39, ES39, in eukaryotic 23 S-like ribosomal RNA was analysed using a combination of chemical and enzymic reagents. Ribosomes were isolated from yeast, wheat, mouse, rat and rabbit, five organisms representing three different eukaryotic kingdoms. The isolated ribosomes were treated with structure-sensitive chemical and enzymic reagents and the modification patterns analysed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The expansion segment was relatively accessible to modification by both enzymic and chemical probes, suggesting that ES39 was exposed on the surface of the ribosomes. The collected modification data were used in secondary structure modelling of the expansion segment. Despite considerable variation in both sequence and length between organisms from different kingdoms, the structure analysis of the expansion segment gave rise to structural fingerprints that allowed identification of homologous structures in ES39 from fungi, plants and mammals. The homologous structures formed an initial helix and an invariant hairpin connected to the initial helix via a long single-stranded loop. The remaining part of the ES39 sequences accounted for most of the length variation seen between the analysed species. This part could form additional, albeit less similar, hairpins. A comparison of ES39 sequences from other fungi, plants and mammals showed that identical structures could be formed in these organisms.
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Affiliation(s)
- Odd Nygård
- School of Life Sciences, Södertörns högskola, Box 4101, S-141 04 Huddinge, Sweden.
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4
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Cannistraro VJ, Kennell D. Ribonuclease YI*, RNA structure studies, and variable single-strand specificities of RNases. Methods Enzymol 2002; 341:175-85. [PMID: 11582777 DOI: 10.1016/s0076-6879(01)41152-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- V J Cannistraro
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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5
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Larsson SL, Nygård O. Proposed secondary structure of eukaryote specific expansion segment 15 in 28S rRNA from mice, rats, and rabbits. Biochemistry 2001; 40:3222-31. [PMID: 11258939 DOI: 10.1021/bi002286q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The expansion segments in eukaryotic ribosomal RNAs are additional RNA sequences not found in the RNA core common to both prokaryotes and eukaryotes. These regions show large species-dependent variations in sequence and size. This makes it difficult to create secondary structure models for the expansion segments exclusively based on phylogenetic sequence comparison. Here we have used a combination of experimental data and computational methods to generate secondary structure models for expansion segment 15 in 28S rRNA in mice, rats, and rabbits. The experimental data were collected using the structure sensitive reagents DMS, CMCT, kethoxal, micrococcal nuclease, RNase T(1), RNase CL3, RNase V(1), and lead(II) acetate. ES15 was folded with the computer program RNAStructure 3.5 using modification data and phylogenetic similarities between different ES15 sequences. This program uses energy minimization to find the most stable secondary structure of an RNA sequence. The presented secondary structure models include several common structural motifs, but they also have characteristics unique to each organism. Overall, the secondary structure models showed indications of an energetically stable but dynamic structure, easily accessible from the solution by the modification reagents, suggesting that the expansion segment is located on the ribosomal surface.
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Affiliation(s)
- S L Larsson
- Natural Science Section, Södertörn University College, S-141 04 Huddinge, Sweden, and Department of Zoological Cell Biology, Arrhenius Laboratories E5, Stockholm University, S-106 91 Stockholm, Sweden
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6
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Blight KJ, Rice CM. Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA. J Virol 1997; 71:7345-52. [PMID: 9311812 PMCID: PMC192079 DOI: 10.1128/jvi.71.10.7345-7352.1997] [Citation(s) in RCA: 167] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The RNA genome of hepatitis C virus (HCV) terminates with a highly conserved 98-base sequence. Enzymatic and chemical approaches were used to define the secondary structure of this 3'-terminal element in RNA transcribed in vitro from cloned cDNA. Both approaches yielded data consistent with a stable stem-loop structure within the 3'-terminal 46 bases. In contrast, the 5' 52 nucleotides of this 98-base element appear to be less ordered and may exist in multiple conformations. Under the experimental conditions tested, interaction between the 3' 98 bases and upstream HCV sequences was not detected. These data provide valuable information for future experiments aimed at identifying host and/or viral proteins which interact with this highly conserved RNA element.
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Affiliation(s)
- K J Blight
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110-1093, USA
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7
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Kolchanov NA, Titov II, Vlassova IE, Vlassov VV. Chemical and computer probing of RNA structure. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 53:131-96. [PMID: 8650302 PMCID: PMC7133174 DOI: 10.1016/s0079-6603(08)60144-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ribonucleic acids (RNAs) are one of the most important types of biopolymers. RNAs play key roles in the storage and multiplication of genetic information. They are important in catalysis and RNA splicing and are the most important steps of translation. This chapter describes experimental methods for probing RNA structure and theoretical methods allowing the prediction of thermodynamically favorable RNA folding. These methods are complementary and together they provide a powerful approach to determine the structure of RNAs. The three-dimensional (tertiary) structure of RNA is formed by hydrogen-bonding among functional groups of nucleosides in different regions of the molecule, by coordination of polyvalent cations, and by stacking between the double-stranded regions present in the RNA. The tertiary structures of only some small RNAs have been determined by high-resolution X-ray crystallographic analysis and nuclear magnetic resonance analysis. The most widely used approach for the investigation of RNA structure is chemical and enzymatic probing, in combination with theoretical methods and phylogenetic studies allowing the prediction of variants of RNA folding. Investigations of RNA structures with different enzymatic and chemical probes can provide detailed data allowing the identification of double-stranded regions of the molecules and nucleotides involved in tertiary interactions.
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Affiliation(s)
- N A Kolchanov
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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8
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Abstract
The higher order folding process of the catalytic RNA derived from the self-splicing intron of Tetrahymena thermophila was monitored with the use of Fe(II)-EDTA-induced free radical chemistry. The overall tertiary structure of the RNA molecule forms cooperatively with the uptake of at least three magnesium ions. Local folding transitions display different metal ion dependencies, suggesting that the RNA tertiary structure assembles through a specific folding intermediate before the catalytic core is formed. Enzymatic activity, assayed with an RNA substrate that is complementary to the catalytic RNA active site, coincides with the cooperative structural transition. The higher order RNA foldings produced by Mg(II), Ca(II), and Sr(II) are similar; however, only the Mg(II)-stabilized RNA is catalytically active. Thus, these results directly demonstrate that divalent metal ions participate in general folding of the ribozyme tertiary structure, and further indicate a more specific involvement of Mg(II) in catalysis.
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Affiliation(s)
- D W Celander
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215
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9
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Faus I, Richardson JP. Structural and functional properties of the segments of lambda cro mRNA that interact with transcription termination factor Rho. J Mol Biol 1990; 212:53-66. [PMID: 2157021 DOI: 10.1016/0022-2836(90)90304-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Termination of transcription at tR1, the Rho-dependent terminator between genes cro and cII of bacteriophage lambda, is dependent upon the structure of segments near the 3' end of the nascent cro gene transcript and on contacts between Rho protein and a 3' proximal segment called rut. The characteristics of the structure of cro RNA in the region from residue 220 to residue 355 in free, isolated RNA and in the presence of Rho or NusA proteins were analyzed by measuring relative rates of reactivity of individual nucleotides with chemicals and enzymes of defined specificities. The results indicate that the rut segments are single-stranded and become blocked to the action of the various probes in the presence of Rho factor. They also show that this region contains two stem-loop structures; one involves the boxB sequence of nutR, the other precedes the tR1 subsite II end points. The results provide direct evidence for a primary binding contact between Rho protein and the rut segment of cro RNA and demonstrate that this binding contact remains stable when the cro RNA is serving as a cofactor for ATP hydrolysis, an observation that is consistent with a mechanism in which Rho maintains contact with the rut region while it makes additional interactions with RNA that are coupled to ATP hydrolysis.
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Affiliation(s)
- I Faus
- Department of Chemistry, Indiana University, Bloomington 47405
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11
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McGarvey P, Helling RB, Lee JY, Engelke DR, el-Gewely MR. Initiation of rrn transcription in chloroplasts of Euglena gracilis bacillaris. Curr Genet 1988; 14:493-500. [PMID: 2852069 DOI: 10.1007/bf00521275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The site of initiation of chloroplast rRNA synthesis was determined by S1-mapping and by sequencing primary rRNA transcripts specifically labeled at their 5'-end. Transcription initiates at a single site 53 nucleotides upstream of the 5'-end of the mature 16S rRNA under all growth conditions examined. The initiation site is within a DNA sequence that is highly homologous to and probably derived from a tRNA gene-region located elsewhere in the chloroplast genome. A nearly identical sequence (102 of 103 nucleotides) is present near the replication origin. The near identity of the two sequences suggests a common mode for control of transcription of the rRNA genes and initiation of chloroplast DNA replication. The related sequence in the tRNA gene-region does not appear to serve as a transcript initiation site.
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Affiliation(s)
- P McGarvey
- Department of Biology, University of Michigan, Ann Arbor 48109
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12
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Yoon JW, Wong AK, Bae YS, Eun HM. An apparent deletion of an oligonucleotide detected by RNA fingerprint in the nondiabetogenic B variant of encephalomyocarditis virus is caused by a point mutation. J Virol 1988; 62:637-40. [PMID: 2826821 PMCID: PMC250583 DOI: 10.1128/jvi.62.2.637-640.1988] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The diabetogenic D variant of encephalomyocarditis virus (EMC-D) was previously shown to be different from the nondiabetogenic B variant of encephalomyocarditis virus (EMC-B) by a single spot in an oligonucleotide fingerprint after RNase T1 digestion of their genomic RNAs. An oligoribonucleotide was missing from EMC-B but was present in EMC-D. The oligoribonucleotide specific to EMC-D was isolated from a two-dimensional polyacrylamide gel and sequenced as 5'-ACAAUCUCACUUUUCCAACAACAG-3'. Molecular hybridizations of EMC-D and EMC-B genomic RNAs with a DNA primer complementary to the EMC-D-specific oligoribonucleotide revealed that the absence of a corresponding spot in EMC-B was due to a point mutation rather than a deletion. By sequencing a cloned cDNA of EMC-B corresponding to the EMC-D-specific oligoribonucleotide, the point mutation was identified as a G for EMC-B and an A for EMC-D transversion at base 9 of the oligonucleotide. Comparative sequence analysis of eight randomly picked RNA segments around the EMC-D-specific oligoribonucleotide revealed that there were no base changes between EMC-D and EMC-B. It is concluded that the diabetogenic EMC-D viral genome differs from the nondiabetogenic EMC-B viral genome by at least a point mutation.
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Affiliation(s)
- J W Yoon
- Department of Microbiology and Infectious Diseases, Julia McFarlane Diabetes Research Center, University of Calgary Health Sciences Centre, Alberta, Canada
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13
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Abstract
Ribonuclease mitochondrial RNA processing, a site-specific endoribonuclease involved in primer RNA metabolism in mammalian mitochondria, requires an RNA component for its activity. On the basis of copurification and selective inactivation with complementary oligonucleotides, a 135-nucleotide RNA species, not encoded in the mitochondrial genome, is identified as the RNA moiety of the endoribonuclease. This finding implies transport of a nucleus-encoded RNA, essential for organelle DNA replication, to the mitochondrial matrix.
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Brinton MA, Fernandez AV, Dispoto JH. The 3'-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 1986; 153:113-21. [PMID: 3016981 DOI: 10.1016/0042-6822(86)90012-7] [Citation(s) in RCA: 182] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The terminal noncoding regions of viral RNA genomes are presumed to contain signal sequences and sometimes also secondary structures involved in regulating viral RNA synthesis. Such signals would be expected to be highly conserved among related viruses. In order to identify replication signal features for flaviviruses we have compared the 3'-terminal nucleotide sequences of West Nile virus (WNV), Saint Louis encephalitis (SLE) virus, and yellow fever virus (YFV) genome RNAs. The existence of a stable 3'-terminal secondary structure was previously predicted by a cDNA sequence obtained from YFV genome RNA. We have confirmed the existence of this structure by direct RNA sequencing methods. Even though the size and shape of the 3'-terminal secondary structure is highly conserved, sequence conservation is restricted to the loop regions of the secondary structure and to 27 nucleotides immediately adjacent to the 5' side of the structure. The regions of conserved sequence represent likely signals for viral polymerase recognition and binding. However, the preservation of the configuration of the secondary structure by a means other than sequence conservation indicate that this structure is important for the survival of the virus. A WNV mutant, which replicates progeny genome RNA more efficiently than parental WNV, was found to have a 3'-genomic sequence identical to that of its parent virus. The sequence change conferring the phenotype of this mutant is therefore located in another region of the genome.
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15
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Blanz PA, Gottschalk M. Systematic Position of Septobasidium, Graphiola and other Basidiomycetes as Deduced on the Basis of their 5S Ribosomal RNA Nucleotide Sequences. Syst Appl Microbiol 1986. [DOI: 10.1016/s0723-2020(86)80159-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Evidence that a capped oligoribonucleotide is the primer for duck hepatitis B virus plus-strand DNA synthesis. J Virol 1986; 57:229-36. [PMID: 2416950 PMCID: PMC252719 DOI: 10.1128/jvi.57.1.229-236.1986] [Citation(s) in RCA: 136] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The plus strand of virion DNA of duck hepatitis B virus possessed, at its 5' terminus, a capped oligoribonucleotide 18 to 19 bases in length. This oligoribonucleotide had a unique 5' end, the heterogeneity in length reflecting two distinct junctions with plus-strand DNA that were 1 base apart. The sequence of the RNA differed from that predicted by the sequence of duck hepatitis B virus upstream of the 5' ends of plus-strand DNA but was identical to a downstream sequence corresponding to the 5' terminus of a major poly(A)+ viral RNA mapped by Büscher and co-workers (Cell 40:717-724, 1985). This RNA transcript is thought to serve as the template (i.e., the pregenome) for minus-strand synthesis via reverse transcription. The results suggest that the pregenome also donates a capped oligoribonucleotide that acts as the primer of plus-strand DNA synthesis, using the minus-strand DNA as template.
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17
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Van Bell CT. The 5S and 5.8S ribosomal RNA sequences of Tetrahymena thermophila and T. pyriformis. THE JOURNAL OF PROTOZOOLOGY 1985; 32:640-4. [PMID: 3934361 DOI: 10.1111/j.1550-7408.1985.tb03093.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The nucleotide sequences of the 5S rRNAs of Tetrahymena thermophila and two strains of T. pyriformis have been determined to be identical. The 5.8S rRNA sequences have also been determined; these sequences correct several errors in an earlier report. The 5.8S rRNAs of the two species differ at a single position. The sequencing results indicate that the species are of recent common ancestry. Molecular evidence that has been interpreted in the past as suggestive of an ancient divergence has been reviewed and found to be consistent with a T. pyriformis complex radiation beginning approximately 30-40 million years ago.
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18
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Phylogeny of the Vibrionaceae, and Recommendation for Two New Genera, Listonella and Shewanella. Syst Appl Microbiol 1985. [DOI: 10.1016/s0723-2020(85)80051-5] [Citation(s) in RCA: 364] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Shelness GS, Williams DL. Secondary structure analysis of apolipoprotein II mRNA using enzymatic probes and reverse transcriptase. Evaluation of primer extension for high resolution structure mapping of mRNA. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39519-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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20
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Ellis B, Jolly J. Purification of a uridine-specific acid nuclease from chicken liver by fast protein liquid chromatography. J Chromatogr A 1985; 326:157-61. [PMID: 4030941 DOI: 10.1016/s0021-9673(01)87441-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A rapid purification procedure for a novel uridine-specific nuclease from chicken liver based on the Pharmacia fast protein liquid chromatography (FPLC) system is presented. The purification was achieved by applying crude extract to a Mono S cation-exchange column equilibrated with 10 mM potassium phosphate buffer (pH 6.0). The enzyme was eluted in 20 min with a potassium chloride gradient at a flow-rate of 2 ml/min. The enzyme was then chromatographed on a Superose 12 size-exclusion column in less than 1 h at a flow-rate of 0.5 ml/min (Kav = 0.77). The enzyme was re-chromatographed on a second Mono S column to concentrate the protein. The uridine-specific nuclease hydrolyzed poly(U) and Escherichia coli 5S RNA. Poly(A) was hydrolyzed by the nuclease less efficiently (about 10% of the poly(U) activity). No hydrolysis was detected with poly(C), poly(G), poly(dT) or poly(dA) as substrate. The speed with which each purification step could be carried out facilitated the determination of optimal chromatographic conditions. We found that the resolution of the Mono S and Superose 12 columns was superior to that of conventional ion exchangers and size-exclusion columns respectively.
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21
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Blanz PA, Gottschalk M. A Comparison of 5S Ribosomal RNA Nucleotide Sequences from Smut Fungi. Syst Appl Microbiol 1984. [DOI: 10.1016/s0723-2020(84)80009-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Garriga G, Lambowitz AM. RNA splicing in neurospora mitochondria: self-splicing of a mitochondrial intron in vitro. Cell 1984; 39:631-41. [PMID: 6096015 DOI: 10.1016/0092-8674(84)90470-7] [Citation(s) in RCA: 157] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We have used Neurospora nuclear mutant cyt-18-1, which accumulates a number of unspliced mitochondrial precursor RNAs, to identify rapidly mitochondrial introns that are self-splicing in vitro. Incubation of deproteinized whole mitochondrial RNA from the mutant with 32P-GTP resulted in strong labeling of a 1.3 kb RNA, subsequently identified as cytochrome b (cob) intron 1, and weaker labeling of additional RNAs. Self-splicing of cob intron 1, including precise cleavage and ligation, was confirmed using an in vitro transcript synthesized from the SP6 promoter. The in vitro splicing reaction was shown to be analogous to that for the Tetrahymena nuclear rRNA intron. Since splicing of cob intron 1 is inhibited in a recessive nuclear mutant, we infer that this essentially RNA-catalyzed splicing reaction must be facilitated by a protein in vivo.
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23
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Ehresmann C, Ehresmann B, Millon R, Ebel JP, Nurse K, Ofengand J. Cross-linking of the anticodon of Escherichia coli and Bacillus subtilis acetylvalyl-tRNA to the ribosomal P site. Characterization of a unique site in both E. coli 16S and yeast 18S ribosomal RNA. Biochemistry 1984; 23:429-37. [PMID: 6422982 DOI: 10.1021/bi00298a006] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The nucleotide residues involved in the cross-link between P site bound acetylvalyl-tRNA (AcVal-tRNA) and 16-18S rRNA have been identified. This cross-link was formed by irradiation of Escherichia coli or Bacillus subtilis AcVal-tRNA bound to the P site of E. coli ribosomes or by irradiation of E. coli AcVal-tRNA bound to the P site of yeast ribosomes. The three cross-linked RNA heterodimers were obtained in 10-35% purity by disruption of the irradiated ribosome-tRNA complex with sodium dodecyl sulfate followed by sucrose gradient centrifugation. After total digestion with RNase T1, and labeling at either the 5'- or the 3'-end, the cross-linked oligomers could be identified and isolated before and after photolytic splitting of the cross-link. One of the oligomers was shown to be UACACACCG, a unique rRNA nonamer present in an evolutionarily conserved region. This oligomer was found in all three heterodimers. The other oligomer of the dimer had the sequence expected for the RNase T1 product encompassing the anticodon of the tRNA used. The precise site of cross-linking was determined by two novel methods. Bisulfite modification of the oligonucleotide dimer converted all C residues to U, except for any cross-linked C which would be resistant by being part of a cyclobutane dimer. Sequencing gel analysis of the UACACACCG oligomer showed that the C residue protected was the 3'-penultimate C residue, C1400 in E. coli rRNA or C1626 in yeast rRNA.(ABSTRACT TRUNCATED AT 250 WORDS)
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Expert-Bezançon A, Milet M, Carbon P. Precise localization of several covalent RNA-RNA cross-link in Escherichia coli 16S RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1983; 136:267-74. [PMID: 6194995 DOI: 10.1111/j.1432-1033.1983.tb07737.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The RNA-RNA cross-linking reagent N-acetyl-N'-(p-glyoxylyl-benzoyl)cystamine, which reacts via its glyoxal residue with guanines not involved in G X C base pairs, has been used to introduce reversible RNA-RNA cross-links into Escherichia coli 16S rRNA. A two-dimensional gel method has been devised for the separation of the cross-linked oligonucleotides, and the precise location of guanines involved in four of these cross-links has been determined by sequencing the oligonucleotides. One cross-link involves guanosines 1315 and 1360 situated in two hairpin end loops of domain III. The other cross-links involves pairs of guanosine situated within the same hairpin end loops.
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25
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Nucleotide sequence of Dictyostelium small nuclear RNA Dd8 not homologous to any other sequenced small nuclear RNA. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44500-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Abstract
The sequences of three transfer RNAs from mosquito cell mitochondria, tRNAArgUCG, tRNAAspGUC, and tRNAIleGAU, determined using a combination of rapid ladder and fingerprinting procedures are reported. These were compared with hamster mitochondrial tRNAArgUCG and tRNAAspGUC determined similarly, and a bovine mitochondrial tRNAIleGAU determined using a somewhat different approach. The primary sequences of the mosquito tRNAs were 35 to 65% homologous to the corresponding mammalian mitochondrial species, and bore little homology to "conventional" (bacterial or eucaryotic cytoplasmic) tRNA. The modification status of the mosquito mitochondrial tRNAs resembled that of mammalian mitochondrial tRNA. The results contribute to the generalization that metazoan mitochondrial tRNA constitutes a distinctive, albeit loosely structured, phylogenetic group.
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Dubin DT, HsuChen CC. The 3'-terminal region of mosquito mitochondrial small ribosomal subunit RNA: sequence and localization of methylated residues. Plasmid 1983; 9:307-20. [PMID: 6867162 DOI: 10.1016/0147-619x(83)90008-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The 3'-terminal 101 residues of the small ribosomal subunit (SSU) RNA of mosquito cell mitochondria have been determined. This stretch includes the four methylated residues of the molecule: an m4C, an m5C, and two m26A residues. The m26A's occur in a typical m26A "arm," and the methylated Cs in the unique subsequence G x m4C . C . m5C . A, which is homologous in position to a conserved methylated GCCCG subsequence of other SSU RNA classes. There is fairly good overall homology between the mosquito mitochondrial sequence and corresponding regions of other SSU RNA classes, except that a domain of 50-100 residues, previously considered universal, is absent. Comparison with mammalian mitochondrial sequences revealed a marked preponderance of transitional base substitutions, supporting earlier evidence that the 3'-terminal region of SSU RNA is under special structural constraints. The extreme 3' end of the mosquito sequence is heterogeneous, three-fourths of the molecules ending in ... GA and one-fourth ending in ... GAA. Evidence is presented indicating that some, at least, of the 3'-terminal A residues may be added post-transcriptionally, as occurs in mammalian mitochondrial systems. Taken together, the results provide modest support for the monophyletic evolutionary origin of insect and mammalian mitochondria from a primitive procaryotic ancestor.
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28
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Chapter 13 Electrophoretic Examination of Enzymes. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/s0301-4770(08)61326-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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29
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30
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Walker WF, Doolittle WF. Redividing the basidiomycetes on the basis of 5S rRNA sequences. Nature 1982; 299:723-4. [PMID: 6985484 DOI: 10.1038/299723a0] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Selker EU, Yanofsky C, Driftmier K, Metzenberg RL, Alzner-DeWeerd B, RajBhandary UL. Dispersed 5S RNA genes in N. crassa: structure, expression and evolution. Cell 1981; 24:819-28. [PMID: 6454495 DOI: 10.1016/0092-8674(81)90107-0] [Citation(s) in RCA: 115] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The 5S RNA genes (5S genes) in N. crassa are not tandemly arranged or tightly clustered as in other eucaryotes that have been examined. 55 RNA or cloned 5S DNA hybridizes to at least 30 different restriction fragments of Neurospora DNA. Of 34 5S DNA clones examined, each contains a single 5S gene. Saturation hybridization analyses indicate that there are about 100 copies of 5S genes in the genome of this organism. We have partially or completely sequenced the 5S region of 15 clones. Both identical and highly divergent 5S coding regions were found. Nine are of one type (alpha). The other six include four different types (beta, beta', gamma and delta) which differ from each other and from the alpha genes to various degrees. Eleven of 15 genes have distinct flanking regions. Analysis of Neurospora 5S RNA showed that it consists of one principal species which matches the alpha-type gene sequence. Additional 5S species corresponding to the less abundant 5S gene types were also detected. The pattern of nucleotide substitutions between the predicted Neurospora 5S RNAs and between these and S. cerevisiae 5S RNA suggests that a particular 5S RNA secondary structure occurs in vivo and is conserved.
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The purification and properties of chicken liver RNase: An enzyme which is useful in distinguishing between cytidylic and uridylic acid residues. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)86006-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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