151
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Abstract
Previous studies have shown that the guanine plus cytosine (G+C) content of ribosomal RNAs (rRNAs) is highly correlated with bacterial growth temperatures. This correlation is strongest in the double-stranded stem regions of the rRNA, a fact that can be explained by selection for increased structural stability at high growth temperatures. In this study, we examined the single-stranded regions of 16S rRNAs. We reasoned that, since these regions of the molecule are subject to less structural constraint than the stem regions, their nucleotide content might simply reflect the overall nucleotide content of the genome. Contrary to this expectation, however, we found that all of the single-stranded regions are characterized by very high adenine (A) and relatively low cytosine (C) contents. Moreover, the nucleotide content of these single-stranded regions is surprisingly constant between species, despite dramatic differences in optimal growth temperatures, and despite large differences in the overall genomic G+C content. This provides compelling evidence for strong stabilizing selection acting on 16S rRNA single-stranded regions. We found that selection favors purines (A+G), and especially adenine (A), in the single-stranded regions of these rRNAs.
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MESH Headings
- Archaea/genetics
- Archaea/growth & development
- Bacteria/genetics
- Bacteria/growth & development
- Base Composition
- Cell Division
- Databases, Nucleic Acid
- Evolution, Molecular
- Genes, Archaeal/genetics
- Genes, Bacterial/genetics
- Genes, rRNA/genetics
- Genome, Archaeal
- Genome, Bacterial
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Ribosomal Proteins/genetics
- Selection, Genetic
- Temperature
- Thermodynamics
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Affiliation(s)
- Huai-chun Wang
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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152
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Abstract
Pyrrolysine is a lysine derivative encoded by the UAG codon in methylamine methyltransferase genes of Methanosarcina barkeri. Near a methyltransferase gene cluster is the pylT gene, which encodes an unusual transfer RNA (tRNA) with a CUA anticodon. The adjacent pylS gene encodes a class II aminoacyl-tRNA synthetase that charges the pylT-derived tRNA with lysine but is not closely related to known lysyl-tRNA synthetases. Homologs of pylS and pylT are found in a Gram-positive bacterium. Charging a tRNA(CUA) with lysine is a likely first step in translating UAG amber codons as pyrrolysine in certain methanogens. Our results indicate that pyrrolysine is the 22nd genetically encoded natural amino acid.
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153
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Abstract
According to small subunit ribosomal RNA (ss rRNA) sequence comparisons all known Archaea belong to the phyla Crenarchaeota, Euryarchaeota, and--indicated only by environmental DNA sequences--to the 'Korarchaeota'. Here we report the cultivation of a new nanosized hyperthermophilic archaeon from a submarine hot vent. This archaeon cannot be attached to one of these groups and therefore must represent an unknown phylum which we name 'Nanoarchaeota' and species, which we name 'Nanoarchaeum equitans'. Cells of 'N. equitans' are spherical, and only about 400 nm in diameter. They grow attached to the surface of a specific archaeal host, a new member of the genus Ignicoccus. The distribution of the 'Nanoarchaeota' is so far unknown. Owing to their unusual ss rRNA sequence, members remained undetectable by commonly used ecological studies based on the polymerase chain reaction. 'N. equitans' harbours the smallest archaeal genome; it is only 0.5 megabases in size. This organism will provide insight into the evolution of thermophily, of tiny genomes and of interspecies communication.
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Affiliation(s)
- Harald Huber
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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154
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Abstract
Although archaeal RNase P RNAs are similar in both sequence and structure to those of Bacteria rather than eukaryotes, and heterologous reconstitution between the Bacillus subtilis RNase P protein and some archaeal RNase P RNAs has been demonstrated, no archaeal protein sequences with similarity to any known bacterial RNase P protein subunit have been identified, and the density of Methanothermobacter thermoautotrophicus RNase P in Cs2SO4 (1.42 g/mL) is inconsistent with a single small bacterial-like protein subunit. Four hypothetical open reading frames (MTH11, MTH687, MTH688, and MTH1618) were identified in the genome of M. thermoautotrophicus that have sequence similarity to four of the nine Saccharomyces cerevisiae RNase P protein subunits: Pop4p, Pop5p, Rpp1p, and Rpr2p, respectively. Polyclonal antisera generated to recombinant Mth11p, Mth687p, Mth688p, and Mth1618p each recognized a protein of the predicted molecular weight in western blots of partially purified M. thermoautotrophicus RNase P, and immunoprecipitated RNase P activity from the same partially purified preparation. RNase P in Archaea is therefore composed of an RNA subunit similar to bacterial RNase P RNA and multiple protein subunits similar to those in the eukaryotic nucleus.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibody Formation
- Blotting, Western
- Cell Nucleus/enzymology
- Centrifugation, Density Gradient
- Cesium/chemistry
- Chlorides/chemistry
- Chromatography, Affinity
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Eukaryotic Cells/enzymology
- Humans
- Methanobacterium/enzymology
- Molecular Sequence Data
- Precipitin Tests
- Protein Subunits
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/metabolism
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- Rabbits
- Recombinant Proteins/immunology
- Recombinant Proteins/isolation & purification
- Recombinant Proteins/metabolism
- Ribonuclease P
- Saccharomyces cerevisiae/enzymology
- Sequence Homology, Amino Acid
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Affiliation(s)
- Thomas A Hall
- Department of Microbiology, North Carolina State University, Raleigh 27695-7615, USA
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155
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Schierling K, Rösch S, Rupprecht R, Schiffer S, Marchfelder A. tRNA 3' end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii. J Mol Biol 2002; 316:895-902. [PMID: 11884130 DOI: 10.1006/jmbi.2001.5395] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' processing pathway. The archaeal RNase Z has a KCl optimum at 5mM, which is in contrast to the intracellular KCl concentration being as high as 4M KCl. The archaeal RNase Z does process 5' extended and intron-containing pretRNAs but with a much lower efficiency than 5' matured, intronless pretRNAs. At least in vitro there is thus no defined order for 5' and 3' processing and splicing. A heterologous precursor tRNA is cleaved efficiently by the archaeal RNase Z. Experiments with precursors containing mutated tRNAs revealed that removal of the anticodon arm reduces cleavage efficiency only slightly, while removal of D and T arm reduces processing effciency drastically, even down to complete inhibition. Comparison with its nuclear and mitochondrial homologs revealed that the substrate specificity of the archaeal RNase Z is narrower than that of the nuclear RNase Z but broader than that of the mitochondrial RNase Z.
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MESH Headings
- Anticodon/genetics
- Base Sequence
- Cell Nucleus/enzymology
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Eukaryotic Cells/enzymology
- Evolution, Molecular
- Haloferax volcanii/enzymology
- Haloferax volcanii/genetics
- Hydrogen-Ion Concentration
- Introns/genetics
- Mitochondria/enzymology
- Mutation/genetics
- Nucleic Acid Conformation
- Osmolar Concentration
- Potassium Chloride/pharmacology
- RNA 3' End Processing
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/genetics
- RNA, Transfer, Tyr/metabolism
- Substrate Specificity
- Temperature
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156
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Tang TH, Rozhdestvensky TS, d'Orval BC, Bortolin ML, Huber H, Charpentier B, Branlant C, Bachellerie JP, Brosius J, Hüttenhofer A. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res 2002; 30:921-30. [PMID: 11842103 PMCID: PMC100335 DOI: 10.1093/nar/30.4.921] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The bulge-helix-bulge (BHB) motif recognised by the archaeal splicing endonuclease is also found in the long processing stems of archaeal rRNA precursors in which it is cleaved to generate pre-16S and pre-23S rRNAs. We show that in two species, Archaeoglobus fulgidus and Sulfolobus solfataricus, representatives from the two major archaeal kingdoms Euryarchaeota and Crenarchaeota, respectively, the pre-rRNA spacers cleaved at the BHB motifs surrounding pre-16S and pre-23S rRNAs subsequently become ligated. In addition, we present evidence that this is accompanied by circularization of ribosomal pre-16S and pre-23S rRNAs in both species. These data reveal a further link between intron splicing and pre-rRNA processing in Archaea, which might reflect a common evolutionary origin of the two processes. One spliced RNA species designated 16S-D RNA, resulting from religation at the BHB motif of 16S pre-rRNA, is a highly abundant and stable RNA which folds into a three-stem structure interrupted by two single-stranded regions as assessed by chemical probing. It spans a region of the pre-rRNA 5' external transcribed spacer exhibiting a highly conserved folding pattern in Archaea. Surprisingly, 16S-D RNA contains structural motifs found in archaeal C/D box small RNAs and binds to the L7Ae protein, a core component of archaeal C/D box RNPs. This supports the notion that it might have an important but still unknown role in pre-rRNA biogenesis or might even target RNA molecules other than rRNA.
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MESH Headings
- Archaeoglobus fulgidus/genetics
- Archaeoglobus fulgidus/metabolism
- Base Sequence
- Electrophoretic Mobility Shift Assay
- Introns
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splicing
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribosomal Proteins/metabolism
- Sequence Homology, Nucleic Acid
- Sulfolobus/genetics
- Sulfolobus/metabolism
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Affiliation(s)
- Thean Hock Tang
- Institut für Experimentelle Pathologie/Molekulare Neurobiologie (ZMBE), Universität Münster, D-48149 Münster, Germany
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157
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Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002; 3:2. [PMID: 11869452 PMCID: PMC65690 DOI: 10.1186/1471-2105-3-2] [Citation(s) in RCA: 1092] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2001] [Accepted: 01/17/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields. RESULTS We have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems. CONCLUSIONS This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.
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MESH Headings
- Base Sequence/genetics
- Databases, Nucleic Acid
- Internet
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA/chemistry
- RNA/genetics
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
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Affiliation(s)
- Jamie J Cannone
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Sankar Subramanian
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
- Department of Biology, Arizona State University, Tempe, AZ 85287-1501, USA
| | - Murray N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
| | - James R Collett
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Lisa M D'Souza
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Yushi Du
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Brian Feng
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Nan Lin
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Lakshmi V Madabusi
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
- Ambion, Inc., Austin, TX 78744-1832, USA
| | - Kirsten M Müller
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Nupur Pande
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Zhidi Shang
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Nan Yu
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Robin R Gutell
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
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158
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Abstract
The European database on SSU rRNA can be consulted via the World WideWeb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also available.
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Affiliation(s)
- Jan Wuyts
- Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerpen, Belgium
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159
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Velázquez E, Trujillo ME, Peix A, Palomo JL, García-Benavides P, Mateos PE, Ventosa A, Martínez-Molina E. Stable low molecular weight RNA analyzed by staircase electrophoresis, a molecular signature for both prokaryotic and eukaryotic microorganisms. Syst Appl Microbiol 2001; 24:490-9. [PMID: 11876355 DOI: 10.1078/0723-2020-00082] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Low-molecular weight RNA (LMW RNA) analysis using staircase electrophoresis was performed for several species of eukaryotic and prokaryotic microorganisms. According to our results, the LMW RNA profiles of archaea and bacteria contain three zones: 5S RNA, class 1 tRNA and class 2 tRNA. In fungi an additional band is included in the LMW RNA profiles, which correspond to the 5.8S RNA. In archaea and bacteria we found that the 5S rRNA zone is characteristic for each genus and the tRNA profile is characteristic for each species. In eukaryotes the combined 5.8S and 5S rRNA zones are characteristic for each genus and, as in prokaryotes, tRNA profiles are characteristic for each species. Therefore, stable low molecular weight RNA, separated by staircase electrophoresis, can be considered a molecular signature for both prokaryotic and eukaryotic microorganisms. Analysis of the data obtained and construction of the corresponding dendrograms afforded relationships between genera and species; these were essentially the same as those obtained with 16S rRNA sequencing (in prokaryotes) and 18S rRNA sequencing (in eukaryotes).
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MESH Headings
- Archaea/chemistry
- Archaea/classification
- Archaea/genetics
- Bacteria/chemistry
- Bacteria/classification
- Bacteria/genetics
- Electrophoresis, Polyacrylamide Gel
- Fungi/chemistry
- Fungi/classification
- Fungi/genetics
- Molecular Weight
- Nucleotide Mapping/methods
- Phylogeny
- RNA, Archaeal/analysis
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Bacterial/analysis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Fungal/analysis
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- Yeasts/chemistry
- Yeasts/classification
- Yeasts/genetics
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Affiliation(s)
- E Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain.
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160
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Clouet d'Orval B, Bortolin ML, Gaspin C, Bachellerie JP. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res 2001; 29:4518-29. [PMID: 11713301 PMCID: PMC92551 DOI: 10.1093/nar/29.22.4518] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Following a search of the Pyrococcus genomes for homologs of eukaryotic methylation guide small nucleolar RNAs, we have experimentally identified in Pyrococcus abyssi four novel box C/D small RNAs predicted to direct 2'-O-ribose methylations onto the first position of the anticodon in tRNALeu(CAA), tRNALeu(UAA), elongator tRNAMet and tRNATrp, respectively. Remarkably, one of them corresponds to the intron of its presumptive target, pre-tRNATrp. This intron is predicted to direct in cis two distinct ribose methylations within the unspliced tRNA precursor, not only onto the first position of the anticodon in the 5' exon but also onto position 39 (universal tRNA numbering) in the 3' exon. The two intramolecular RNA duplexes expected to direct methylation, which both span an exon-intron junction in pre-tRNATrp, are phylogenetically conserved in euryarchaeotes. We have experimentally confirmed the predicted guide function of the box C/D intron in halophile Haloferax volcanii by mutagenesis analysis, using an in vitro splicing/RNA modification assay in which the two cognate ribose methylations of pre-tRNATrp are faithfully reproduced. Euryarchaeal pre-tRNATrp should provide a unique system to further investigate the molecular mechanisms of RNA-guided ribose methylation and gain new insights into the origin and evolution of the complex family of archaeal and eukaryotic box C/D small RNAs.
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MESH Headings
- Base Sequence
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- Genome, Archaeal
- Introns/genetics
- Methylation
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Nucleosides/genetics
- Nucleosides/metabolism
- Nucleotides/genetics
- Nucleotides/metabolism
- Phylogeny
- Plasmids/genetics
- Pyrococcus/genetics
- Pyrococcus/metabolism
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Trp/genetics
- RNA, Transfer, Trp/metabolism
- Ribose/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- B Clouet d'Orval
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099 du CNRS, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
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161
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Abstract
Comparisons of complete 16S ribosomal RNA sequences have been used to confirm, refine and extend earlier concepts of archaebacterial phylogeny. The archaebacteria fall naturally into two major branches or divisions, I--the sulfur-dependent thermophilic archaebacteria, and II--the methanogenic archaebacteria and their relatives. Division I comprises a relatively closely related and phenotypically homogeneous collection of thermophilic sulfur-dependent species--encompassing the genera Sulfolobus, Thermoproteus, Pyrodictium and Desulfurococcus. The organisms of Division II, however, form a less compact grouping phylogenetically, and are also more diverse in phenotype. All three of the (major) methanogen groups are found in Division II, as are the extreme halophiles and two types of thermoacidophiles, Thermoplasma acidophilum and Thermococcus celer. This last species branches sufficiently deeply in the Division II line that it might be considered to represent a separate, third Division. However, both the extreme halophiles and Tp. acidophilum branch within the cluster of methanogens. The extreme halophiles are specifically related to the Methanomicrobiales, to the exclusion of both the Methanococcales and the Methanobacteriales. Tp. acidophilum is peripherally related to the halophile-Methanomicrobiales group. By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Alternative proposals for archaebacterial phylogeny, not based upon sequence evidence, are discussed and evaluated. In particular, proposals to rename (reclassify) various subgroups of the archaebacteria as new kingdoms are found wanting, for both their lack of proper experimental support and the taxonomic confusion they introduce.
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MESH Headings
- Archaea/chemistry
- Archaea/classification
- Archaea/genetics
- Bacteria/classification
- Bacteria/genetics
- Base Sequence
- Biological Evolution
- Eukaryotic Cells/chemistry
- Eukaryotic Cells/classification
- Eukaryotic Cells/physiology
- Euryarchaeota/chemistry
- Euryarchaeota/classification
- Euryarchaeota/genetics
- Membrane Lipids/analysis
- Molecular Sequence Data
- Phylogeny
- RNA, Archaeal/analysis
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, RNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- C R Woese
- Department of Genetics and Development, University of Illinois, Urbana 61801, USA
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162
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Tishchenko SV, Vassilieva JM, Platonova OB, Serganov AA, Fomenkova NP, Mudrik ES, Piendl W, Ehresmann C, Ehresmann B, Garber MB. Isolation, crystallization, and investigation of ribosomal protein S8 complexed with specific fragments of rRNA of bacterial or archaeal origin. Biochemistry (Mosc) 2001; 66:948-53. [PMID: 11703173 DOI: 10.1023/a:1012353122174] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The core ribosomal protein S8 binds to the central domain of 16S rRNA independently of other ribosomal proteins and is required for assembling the 30S subunit. It has been shown with E. coli ribosomes that a short rRNA fragment restricted by nucleotides 588-602 and 636-651 is sufficient for strong and specific protein S8 binding. In this work, we studied the complexes formed by ribosomal protein S8 from Thermus thermophilus and Methanococcus jannaschii with short rRNA fragments isolated from the same organisms. The dissociation constants of the complexes of protein S8 with rRNA fragments were determined. Based on the results of binding experiments, rRNA fragments of different length were designed and synthesized in preparative amounts in vitro using T7 RNA-polymerase. Stable S8-RNA complexes were crystallized. Crystals were obtained both for homologous bacterial and archaeal complexes and for hybrid complexes of archaeal protein with bacterial rRNA. Crystals of the complex of protein S8 from M. jannaschii with the 37-nucleotide rRNA fragment from the same organism suitable for X-ray analysis were obtained.
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Affiliation(s)
- S V Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia.
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163
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Tishchenko S, Nikulin A, Fomenkova N, Nevskaya N, Nikonov O, Dumas P, Moine H, Ehresmann B, Ehresmann C, Piendl W, Lamzin V, Garber M, Nikonov S. Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii. J Mol Biol 2001; 311:311-24. [PMID: 11478863 DOI: 10.1006/jmbi.2001.4877] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structure of ribosomal protein S8 bound to its target 16 S rRNA from a hyperthermophilic archaeon Methanococcus jannaschii has been determined at 2.6 A resolution. The protein interacts with the minor groove of helix H21 at two sites located one helical turn apart, with S8 forming a bridge over the RNA major groove. The specificity of binding is essentially provided by the C-terminal domain of S8 and the highly conserved nucleotide core, characterized by two dinucleotide platforms, facing each other. The first platform (A595-A596), which is the less phylogenetically and structurally constrained, does not directly contact the protein but has an important shaping role in inducing cross-strand stacking interactions. The second platform (U641-A642) is specifically recognized by the protein. The universally conserved A642 plays a pivotal role by ensuring the cohesion of the complex organization of the core through an array of hydrogen bonds, including the G597-C643-U641 base triple. In addition, A642 provides the unique base-specific interaction with the conserved Ser105, while the Thr106 - Thr107 peptide link is stacked on its purine ring. Noteworthy, the specific recognition of this tripeptide (Thr-Ser-Thr/Ser) is parallel to the recognition of an RNA tetraloop by a dinucleotide platform in the P4-P6 ribozyme domain of group I intron. This suggests a general dual role of dinucleotide platforms in recognition of RNA or peptide motifs. One prominent feature is that conserved side-chain amino acids, as well as conserved bases, are essentially involved in maintaining tertiary folds. The specificity of binding is mainly driven by shape complementarity, which is increased by the hydrophobic part of side-chains. The remarkable similarity of this complex with its homologue in the T. thermophilus 30 S subunit indicates a conserved interaction mode between Archaea and Bacteria.
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MESH Headings
- Amino Acid Sequence
- Archaeal Proteins/chemistry
- Archaeal Proteins/metabolism
- Bacteria/chemistry
- Bacteria/genetics
- Base Sequence
- Binding Sites
- Conserved Sequence/genetics
- Crystallography, X-Ray
- Evolution, Molecular
- Humans
- Hydrogen Bonding
- Methanococcus/chemistry
- Methanococcus/genetics
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- Protein Structure, Secondary
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Sequence Alignment
- Substrate Specificity
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Affiliation(s)
- S Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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164
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Abstract
Analysis of the Haloarcula marismortui large ribosomal subunit has revealed a common RNA structure that we call the kink-turn, or K-turn. The six K-turns in H.marismortui 23S rRNA superimpose with an r.m.s.d. of 1.7 A. There are two K-turns in the structure of Thermus thermophilus 16S rRNA, and the structures of U4 snRNA and L30e mRNA fragments form K-turns. The structure has a kink in the phosphodiester backbone that causes a sharp turn in the RNA helix. Its asymmetric internal loop is flanked by C-G base pairs on one side and sheared G-A base pairs on the other, with an A-minor interaction between these two helical stems. A derived consensus secondary structure for the K-turn includes 10 consensus nucleotides out of 15, and predicts its presence in the 5'-UTR of L10 mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP. Five K-turns in 23S rRNA interact with nine proteins. While the observed K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way.
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Affiliation(s)
- D.J. Klein
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA Corresponding author e-mail:
D.J.Klein and T.M.Schmeing contributed equally to this work
| | - T.M. Schmeing
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA Corresponding author e-mail:
D.J.Klein and T.M.Schmeing contributed equally to this work
| | - P.B. Moore
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA Corresponding author e-mail:
D.J.Klein and T.M.Schmeing contributed equally to this work
| | - T.A. Steitz
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA Corresponding author e-mail:
D.J.Klein and T.M.Schmeing contributed equally to this work
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165
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Gorodkin J, Stricklin SL, Stormo GD. Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res 2001; 29:2135-44. [PMID: 11353083 PMCID: PMC55461 DOI: 10.1093/nar/29.10.2135] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2001] [Revised: 03/14/2001] [Accepted: 03/27/2001] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression is often accomplished by proteins binding to specific sequence motifs in mRNA molecules, to affect their translation or stability. The motifs are often composed of a combination of sequence and structural constraints such that the overall structure is preserved even though much of the primary sequence is variable. While several methods exist to discover transcriptional regulatory sites in the DNA sequences of coregulated genes, the RNA motif discovery problem is much more difficult because of covariation in the positions. We describe the combined use of two approaches for RNA structure prediction, FOLDALIGN and COVE, that together can discover and model stem-loop RNA motifs in unaligned sequences, such as UTRs from post-transcriptionally coregulated genes. We evaluate the method on two datasets, one a section of rRNA genes with randomly truncated ends so that a global alignment is not possible, and the other a hyper-variable collection of IRE-like elements that were inserted into randomized UTR sequences. In both cases the combined method identified the motifs correctly, and in the rRNA example we show that it is capable of determining the structure, which includes bulge and internal loops as well as a variable length hairpin loop. Those automated results are quantitatively evaluated and found to agree closely with structures contained in curated databases, with correlation coefficients up to 0.9. A basic server, Stem-Loop Align SearcH (SLASH), which will perform stem-loop searches in unaligned RNA sequences, is available at http://www.bioinf.au.dk/slash/.
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Affiliation(s)
- J Gorodkin
- Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK-8000 Aarhus C, Denmark
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166
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Bhuiyan SH, Pakhomova ON, Hinck AP, Zwieb C. Complexes with truncated RNAs from the large domain of Archaeoglobus fulgidus signal recognition particle. FEMS Microbiol Lett 2001; 198:105-10. [PMID: 11430398 DOI: 10.1111/j.1574-6968.2001.tb10626.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Protein SRP19 is an important component of the signal recognition particle (SRP) as it promotes assembly of protein SRP54 with SRP RNA and recognizes a tetranucleotide loop. Structural features and RNA binding activities of SRP19 of the hyperthermophilic archaeon Archaeoglobus fulgidus were investigated. An updated alignment of SRP19 sequences predicted three conserved regions and two alpha-helices. With Af-SRP RNA the Af-SRP54 protein assembled into an A. fulgidus SRP which remained intact for many hours. Stable complexes were formed between Af-SRP19 and truncated SRP RNAs, including a 36-residue fragment representing helix 6 of A. fulgidus SRP RNA.
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Affiliation(s)
- S H Bhuiyan
- Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 75708-3154, USA
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167
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Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc Natl Acad Sci U S A 2001; 98:4899-903. [PMID: 11296253 PMCID: PMC33135 DOI: 10.1073/pnas.081082398] [Citation(s) in RCA: 550] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2001] [Indexed: 11/18/2022] Open
Abstract
Analysis of the 2.4-A resolution crystal structure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2' OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3' terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures.
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MESH Headings
- Adenosine/chemistry
- Adenosine/genetics
- Adenosine/metabolism
- Base Pairing
- Binding Sites
- Conserved Sequence/genetics
- Haloarcula marismortui/chemistry
- Haloarcula marismortui/genetics
- Hydrogen Bonding
- Models, Molecular
- Mutation/genetics
- Nucleic Acid Conformation
- Protein Subunits
- RNA Stability
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Solvents
- Structure-Activity Relationship
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Affiliation(s)
- P Nissen
- Department of Molecular Biophysics and Biochemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA
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168
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Belova L, Tenson T, Xiong L, McNicholas PM, Mankin AS. A novel site of antibiotic action in the ribosome: interaction of evernimicin with the large ribosomal subunit. Proc Natl Acad Sci U S A 2001; 98:3726-31. [PMID: 11259679 PMCID: PMC31120 DOI: 10.1073/pnas.071527498] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evernimicin (Evn), an oligosaccharide antibiotic, interacts with the large ribosomal subunit and inhibits bacterial protein synthesis. RNA probing demonstrated that the drug protects a specific set of nucleotides in the loops of hairpins 89 and 91 of 23S rRNA in bacterial and archaeal ribosomes. Spontaneous Evn-resistant mutants of Halobacterium halobium contained mutations in hairpins 89 and 91 of 23S rRNA. In the ribosome tertiary structure, rRNA residues involved in interaction with the drug form a tight cluster that delineates the drug-binding site. Resistance mutations in the bacterial ribosomal protein L16, which is shown to be homologous to archaeal protein L10e, cluster to the same region as the rRNA mutations. The Evn-binding site overlaps with the binding site of initiation factor 2. Evn inhibits activity of initiation factor 2 in vitro, suggesting that the drug interferes with formation of the 70S initiation complex. The site of Evn binding and its mode of action are distinct from other ribosome-targeted antibiotics. This antibiotic target site can potentially be used for the development of new antibacterial drugs.
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MESH Headings
- Aminoglycosides
- Anti-Bacterial Agents/pharmacology
- Binding Sites
- Drug Resistance, Microbial/genetics
- Halobacterium salinarum/chemistry
- Halobacterium salinarum/genetics
- Halobacterium salinarum/isolation & purification
- Models, Molecular
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- RNA, Archaeal/chemistry
- RNA, Archaeal/drug effects
- RNA, Bacterial/chemistry
- RNA, Bacterial/drug effects
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/drug effects
- RNA, Ribosomal, 23S/genetics
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Affiliation(s)
- L Belova
- Center for Pharmaceutical Biotechnology, M/C 870, University of Illinois, 900 South Ashland Avenue, Chicago, IL 60607, USA
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169
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Abstract
Eukaryal tRNA splicing endonucleases use the mature domains of pre-tRNAs as their primary recognition elements. However, they can also cleave in a mode that is independent of the mature domain, when substrates are able to form the bulge-helix-bulge structure (BHB), which is cleaved by archaeal tRNA endonucleases. We present evidence that the eukaryal enzymes cleave their substrates after forming a structure that resembles the BHB. Consequently, these enzymes can cleave substrates that lack the mature domain altogether. That raises the possibility that these enzymes could also cleave non-tRNA substrates that already have a BHB. As predicted, they can do so, both in vitro and in vivo.
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Affiliation(s)
- P Fruscoloni
- Istituto di Biologia Cellulare, CNR, Campus 'A. Buzzati-Traverso', Via E. Ramarini, 32, 00016 Monterotondo Scalo (RM), Italy
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170
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Kirpekar F, Krogh TN. RNA fragmentation studied in a matrix-assisted laser desorption/ionisation tandem quadrupole/orthogonal time-of-flight mass spectrometer. Rapid Commun Mass Spectrom 2001; 15:8-14. [PMID: 11135418 DOI: 10.1002/1097-0231(20010115)15:1<8::aid-rcm185>3.0.co;2-s] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have studied the fragmentation behaviour of short, singly protonated oligoribonucleotides on a MALDI Qq-TOF instrument with the aim of using this instrumental set-up to characterise modifications of RNA molecules. Individual ion species from enzymatically generated mixtures were isolated in one quadrupole and subjected to collision-induced dissociation in a second quadrupole followed by separation of the resulting product ions in an orthogonal time-of-flight mass analyser. Complex spectra were generally observed with nearly all types of cleavages along the phosphodiester backbone and of the N-glycosidic bonds (and combinations of these) occurring, albeit at different relative intensities. The most labile part of the backbone was found to be the 5'-P-O bond, resulting in c- and y-ions. Loss of neutral cytosine and guanine occurred equally often, whereas neutral loss of adenosine was less prevalent. Loss of uracil, either neutral or charged species, was not observed. Because the fragmentation pattern observed here is significantly different from what has been reported for singly protonated oligodeoxyribonucleotides, we suggest that the 2'-substituent in the sugar plays a central role in the fragmentation mechanisms of nucleic acids. Finally, we used the acquired knowledge about oligoribonucleotide fragmentation to characterise an in vivo methylated oligoribonucleotide by tandem mass spectrometry.
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MESH Headings
- Base Sequence
- Geobacillus stearothermophilus/genetics
- Geobacillus stearothermophilus/metabolism
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/genetics
- Oligoribonucleotides/metabolism
- Protons
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Sulfolobus acidocaldarius/genetics
- Sulfolobus acidocaldarius/metabolism
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Affiliation(s)
- F Kirpekar
- Department of Biochemistry and Molecular Biology, Odense University SDU, Campusvej 55, DK-5230 Odense M, Denmark.
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171
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MESH Headings
- Archaea/enzymology
- Archaea/genetics
- Archaeal Proteins/chemistry
- Archaeal Proteins/classification
- Archaeal Proteins/genetics
- Archaeal Proteins/isolation & purification
- Bacteria/enzymology
- Bacteria/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/classification
- Bacterial Proteins/genetics
- Bacterial Proteins/isolation & purification
- Base Sequence
- Chloroplasts/enzymology
- Endoribonucleases/chemistry
- Endoribonucleases/classification
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Evolution, Molecular
- Fungal Proteins/chemistry
- Fungal Proteins/classification
- Fungal Proteins/genetics
- Fungal Proteins/isolation & purification
- HeLa Cells/enzymology
- Humans
- Molecular Sequence Data
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/classification
- Neoplasm Proteins/genetics
- Neoplasm Proteins/isolation & purification
- Nucleic Acid Conformation
- Organelles/enzymology
- Plant Proteins/chemistry
- Plant Proteins/classification
- Plant Proteins/isolation & purification
- Protein Subunits
- RNA, Archaeal/chemistry
- RNA, Archaeal/classification
- RNA, Archaeal/genetics
- RNA, Archaeal/isolation & purification
- RNA, Bacterial/chemistry
- RNA, Bacterial/classification
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Catalytic/chemistry
- RNA, Catalytic/classification
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Fungal/chemistry
- RNA, Fungal/classification
- RNA, Fungal/genetics
- RNA, Fungal/isolation & purification
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/classification
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Ribonuclease P
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/classification
- Ribonucleoproteins/genetics
- Ribonucleoproteins/isolation & purification
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Terminology as Topic
- Zea mays/enzymology
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Affiliation(s)
- S Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA.
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172
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Kim H, Honda D, Hanada S, Kanamori N, Shibata S, Miyaki T, Nakamura K, Oyaizu H. A deeply branched novel phylotype found in Japanese paddy soils. Microbiology (Reading) 2000; 146 ( Pt 9):2309-2315. [PMID: 10974118 DOI: 10.1099/00221287-146-9-2309] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Novel 16S rDNA clones which possibly constitute a sister clade from the two known archaeal lineages, Crenarchaeota and Euryarchaeota, were found in paddy soil environments. Overall signature sequences showed that the clone sequences shared a majority of signature sequence features with the Archaea and Eukarya. However, there were at least nine nucleotides which distinguished the novel clones from the domains Archaea and Eukarya. Phylogenetic trees, drawn by maximum-parsimony, neighbour-joining and maximum-likelihood methods, also supported the unique phylogenetic position of the clones. Both signature sequence and phylogenetic analyses strongly suggest that the novel organisms constitute a new group and their phylogenetic positions are distant from the Crenarchaeota and Euryarchaeota. A specific primer set was designed to detect the presence of the novel group of organisms in terrestrial environments. Specific DNA fragments were amplified from all paddy soil DNAs, suggesting that the novel organisms are widely distributed in rice paddy fields in Japan.
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MESH Headings
- Archaea/classification
- Archaea/genetics
- Archaea/isolation & purification
- Base Composition
- Base Sequence
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Japan
- Molecular Sequence Data
- Nucleic Acid Conformation
- Oryza
- Phylogeny
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
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Affiliation(s)
- Hongik Kim
- Microbial Resources and Chemotaxonomy Research Group, National Institute of Bioscience and Human-technology, Agency of Industrial Science and Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan3
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan
| | - Daiske Honda
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan
| | - Satoshi Hanada
- Microbial Resources and Chemotaxonomy Research Group, National Institute of Bioscience and Human-technology, Agency of Industrial Science and Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan3
| | - Norihiro Kanamori
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan
| | - Satoshi Shibata
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan
| | - Taro Miyaki
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan
| | - Kazunori Nakamura
- Microbial Resources and Chemotaxonomy Research Group, National Institute of Bioscience and Human-technology, Agency of Industrial Science and Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan3
| | - Hiroshi Oyaizu
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan
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173
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Abstract
Ribosomes, the cellular factories that manufacture proteins, contain both RNA and protein, but exactly how all of the different ribosomal components contribute to protein synthesis is still not clear. Now, as Thomas Cech explains in his Perspective, atomic resolution of the structure of the large ribosomal subunit reveals that, as predicted by those convinced of a prebiotic RNA world, RNA is the catalytic component with proteins being the structural units that support and stabilize it (Ban et al., Nissen et al., Muth et al.).
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MESH Headings
- Adenine/chemistry
- Adenine/metabolism
- Archaeal Proteins/chemistry
- Archaeal Proteins/metabolism
- Binding Sites
- Catalysis
- Crystallography, X-Ray
- Evolution, Molecular
- Haloarcula marismortui/chemistry
- Haloarcula marismortui/ultrastructure
- Hydrogen-Ion Concentration
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Biosynthesis
- RNA, Archaeal/chemistry
- RNA, Archaeal/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
- T R Cech
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA.
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174
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Abstract
The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior.
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MESH Headings
- Archaeal Proteins/chemistry
- Archaeal Proteins/metabolism
- Base Sequence
- Binding Sites
- Conserved Sequence
- Crystallography, X-Ray
- Haloarcula marismortui/chemistry
- Haloarcula marismortui/ultrastructure
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Conformation
- Protein Folding
- RNA, Archaeal/chemistry
- RNA, Archaeal/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/ultrastructure
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Affiliation(s)
- N Ban
- Department of Molecular Biophysics & Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA
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175
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Abstract
Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coli) playing the same general base role as histidine-57 in chymotrypsin. The unusual pK(a) (where K(a) is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e.
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MESH Headings
- Archaeal Proteins/chemistry
- Archaeal Proteins/metabolism
- Base Pairing
- Base Sequence
- Binding Sites
- Catalysis
- Crystallization
- Evolution, Molecular
- Haloarcula marismortui/chemistry
- Haloarcula marismortui/metabolism
- Haloarcula marismortui/ultrastructure
- Hydrogen Bonding
- Hydrogen-Ion Concentration
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Oligonucleotides/metabolism
- Peptide Biosynthesis
- Peptides/metabolism
- Peptidyl Transferases/antagonists & inhibitors
- Peptidyl Transferases/chemistry
- Peptidyl Transferases/metabolism
- Phosphates/chemistry
- Phosphates/metabolism
- Protein Conformation
- Puromycin/metabolism
- RNA, Archaeal/chemistry
- RNA, Archaeal/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
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Affiliation(s)
- P Nissen
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA
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176
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Abstract
The U-turn is a well-known RNA motif characterized by a sharp reversal of the RNA backbone following a single-stranded uridine base. In experimentally determined U-turn motifs, the nucleotides 3' to the turn are frequently involved in tertiary interactions, rendering this motif particularly attractive in RNA modeling and functional studies. The U-turn signature is composed of an UNR sequence pattern flanked by a Y:Y, Y:A (Y=pyrimidine) or G:A base juxtaposition. We have identified 33 potential UNR-type U-turns and 25 related GNRA-type U-turns in a large set of aligned 16 S and 23 S rRNA sequences. U-turn candidates occur in hairpin loops (34 times) as well as in internal and multi-stem loops (24 times). These are classified into ten families based on loop type, sequence pattern (UNR or GNRA) and the nature of the closing base juxtaposition. In 13 cases, the bases on the 3' side of the turn, or on the immediate 5' side, are involved in tertiary covariations, making these sites strong candidates for tertiary interactions.
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MESH Headings
- Animals
- Anticodon/chemistry
- Anticodon/genetics
- Base Pairing/genetics
- Base Sequence
- Chloroplasts/genetics
- Consensus Sequence/genetics
- Hydrogen Bonding
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Sequence Alignment
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Affiliation(s)
- R R Gutell
- Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX, 78712-1095, USA.
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177
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Rodriguez-Fonseca C, Phan H, Long KS, Porse BT, Kirillov SV, Amils R, Garrett RA. Puromycin-rRNA interaction sites at the peptidyl transferase center. RNA 2000; 6:744-54. [PMID: 10836795 PMCID: PMC1369954 DOI: 10.1017/s1355838200000091] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The binding site of puromycin was probed chemically in the peptidyl-transferase center of ribosomes from Escherichia coli and of puromycin-hypersensitive ribosomes from the archaeon Haloferax gibbonsii. Several nucleotides of the 23S rRNAs showed altered chemical reactivities in the presence of puromycin. They include A2439, G2505, and G2553 for E. coli, and G2058, A2503, G2505, and G2553 for Hf. gibbonsii (using the E. coli numbering system). Reproducible enhanced reactivities were also observed at A508 and A1579 within domains I and III, respectively, of E. coli 23S rRNA. In further experiments, puromycin was shown to produce a major reduction in the UV-induced crosslinking of deacylated-(2N3A76)tRNA to U2506 within the P' site of E. coli ribosomes. Moreover, it strongly stimulated the putative UV-induced crosslink between a streptogramin B drug and m2A2503/psi2504 at an adjacent site in E. coli 23S rRNA. These data strongly support the concept that puromycin, along with other peptidyl-transferase antibiotics, in particular the streptogramin B drugs, bind to an RNA structural motif that contains several conserved and accessible base moieties of the peptidyl transferase loop region. This streptogramin motif is also likely to provide binding sites for the 3' termini of the acceptor and donor tRNAs. In contrast, the effects at A508 and A1579, which are located at the exit site of the peptide channel, are likely to be caused by a structural effect transmitted along the peptide channel.
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MESH Headings
- Base Sequence
- Binding Sites
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Haloferax/genetics
- Haloferax/metabolism
- Molecular Sequence Data
- Peptidyl Transferases/chemistry
- Peptidyl Transferases/metabolism
- Puromycin/chemistry
- Puromycin/metabolism
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Substrate Specificity
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Affiliation(s)
- C Rodriguez-Fonseca
- RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Denmark
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178
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Abstract
In eukaryotes, dozens of posttranscriptional modifications are directed to specific nucleotides in ribosomal RNAs (rRNAs) by small nucleolar RNAs (snoRNAs). We identified homologs of snoRNA genes in both branches of the Archaea. Eighteen small sno-like RNAs (sRNAs) were cloned from the archaeon Sulfolobus acidocaldarius by coimmunoprecipitation with archaeal fibrillarin and NOP56, the homologs of eukaryotic snoRNA-associated proteins. We trained a probabilistic model on these sRNAs to search for more sRNAs in archaeal genomic sequences. Over 200 additional sRNAs were identified in seven archaeal genomes representing both the Crenarchaeota and the Euryarchaeota. snoRNA-based rRNA processing was therefore probably present in the last common ancestor of Archaea and Eukarya, predating the evolution of a morphologically distinct nucleolus.
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MESH Headings
- Archaea/genetics
- Archaeal Proteins/genetics
- Base Sequence
- Chromosomal Proteins, Non-Histone/genetics
- Cloning, Molecular
- Genome, Archaeal
- Methylation
- Models, Statistical
- Molecular Sequence Data
- Nuclear Proteins/genetics
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Sulfolobus acidocaldarius/genetics
- RNA, Small Untranslated
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Affiliation(s)
- A D Omer
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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179
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Gaspin C, Cavaillé J, Erauso G, Bachellerie JP. Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J Mol Biol 2000; 297:895-906. [PMID: 10736225 DOI: 10.1006/jmbi.2000.3593] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribose methylation is a prevalent type of nucleotide modification in rRNA. Eukaryotic rRNAs display a complex pattern of ribose methylations, amounting to 55 in yeast Saccharomyces cerevisiae and about 100 in vertebrates. Ribose methylations of eukaryotic rRNAs are each guided by a cognate small RNA, belonging to the family of box C/D antisense snoRNAs, through transient formation of a specific base-pairing at the rRNA modification site. In prokaryotes, the pattern of rRNA ribose methylations has been fully characterized in a single species so far, Escherichia coli, which contains only four ribose methylated rRNA nucleotides. However, the hyperthermophile archaeon Sulfolobus solfataricus contains, like eukaryotes, a large number of (yet unmapped) rRNA ribose methylations and homologs of eukaryotic box C/D small nucleolar ribonuclear proteins have been identified in archaeal genomes. We have therefore searched archaeal genomes for potential homologs of eukaryotic methylation guide small nucleolar RNAs, by combining searches for structured motifs with homology searches. We have identified a family of 46 small RNAs, conserved in the genomes of three hyperthermophile Pyrococcus species, which we have experimentally characterized in Pyrococcus abyssi. The Pyrococcus small RNAs, the first reported homologs of methylation guide small nucleolar RNAs in organisms devoid of a nucleus, appear as a paradigm of minimalist box C/D antisense RNAs. They differ from their eukaryotic homologs by their outstanding structural homogeneity, extended consensus box motifs and the quasi-systematic presence of two (instead of one) rRNA antisense elements. Remarkably, for each small RNA the two antisense elements always match rRNA sequences close to each other in rRNA structure, suggesting an important role in rRNA folding. Only a few of the predicted P. abyssi rRNA ribose methylations have been detected so far. Further analysis of these archaeal small RNAs could provide new insights into the origin and functions of methylation guide small nucleolar RNAs and illuminate the still elusive role of rRNA ribose methylations.
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MESH Headings
- Base Sequence
- Consensus Sequence/genetics
- Databases, Factual
- Eukaryotic Cells/metabolism
- Genes, Archaeal/genetics
- Genome, Archaeal
- Methylation
- Molecular Sequence Data
- Nucleic Acid Conformation
- Open Reading Frames/genetics
- Physical Chromosome Mapping
- Pyrococcus/genetics
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribose/metabolism
- Sequence Homology, Nucleic Acid
- Software
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Affiliation(s)
- C Gaspin
- Laboratoire de Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, 31326, France
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180
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Briones C, Amils R. Nucleotide sequence of the 235 rRNA from Haloferax mediterranei and phylogenetic analysis of halophilic archaea based on LSU rRNA. Syst Appl Microbiol 2000; 23:124-31. [PMID: 10879986 DOI: 10.1016/s0723-2020(00)80053-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
23S rRNA gene from the halophilic archaeon Haloferax mediterranei (strain ATCC 33500) was cloned and sequenced. Proceeding from the 2,912 nucleotides long sequence, the secondary structure of Haloferax genus large subunit rRNA was proposed. Haloferax mediterranei intergenic spacers 16S/23S and 23S/5S were also sequenced, and found to be 382 and 116 nucleotides long respectively. The 16S/23S spacer showed an Ala-tRNA intervening sequence, which is a common feature in Euryarchaeota. Sequence analysis of 23S rRNA and 16S rRNA was performed for the six organisms from the family Halobacteriaceae with both available gene sequences. Phylogenetic trees with completely different topology were obtained using both molecules.
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MESH Headings
- Base Sequence
- DNA, Archaeal/genetics
- DNA, Ribosomal Spacer/genetics
- Genes, rRNA
- Halobacteriales/classification
- Halobacteriales/genetics
- Haloferax mediterranei/classification
- Haloferax mediterranei/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
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Affiliation(s)
- C Briones
- Centro de Astrobiologia, INTA-CSIC, Madrid, Spain
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181
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Abstract
We present a method to screen RNA for posttranscriptional modifications based on Matrix Assisted Laser Desorption/Ionization mass spectrometry (MALDI-MS). After the RNA is digested to completion with a nucleotide-specific RNase, the fragments are analyzed by mass spectrometry. A comparison of the observed mass data with the data predicted from the gene sequence identifies fragments harboring modified nucleotides. Fragments larger than dinucleotides were valuable for the identification of posttranscriptional modifications. A more refined mapping of RNA modifications can be obtained by using two RNases in parallel combined with further fragmentation by Post Source Decay (PSD). This approach allows fast and sensitive screening of a purified RNA for posttranscriptional modification, and has been applied on 5S rRNA from two thermophilic microorganisms, the bacterium Bacillus stearothermophilus and the archaeon Sulfolobus acidocaldarius, as well as the halophile archaea Halobacterium halobium and Haloarcula marismortui. One S. acidocaldarius posttranscriptional modification was identified and was further characterized by PSD as a methylation of cytidine32. The modified C is located in a region that is clearly conserved with respect to both sequence and position in B. stearothermophilus and H. halobium and to some degree also in H. marismortui. However, no analogous modification was identified in the latter three organisms. We further find that the 5' end of H. halobium 5S rRNA is dephosphorylated, in contrast to the other 5S rRNA species investigated. The method additionally gives an immediate indication of whether the expected RNA sequence is in agreement with the observed fragment masses. Discrepancies with two of the published 5S rRNA sequences were identified and are reported here.
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MESH Headings
- Base Sequence
- Geobacillus stearothermophilus/genetics
- Geobacillus stearothermophilus/metabolism
- Haloarcula marismortui/genetics
- Haloarcula marismortui/metabolism
- Halobacterium salinarum/genetics
- Halobacterium salinarum/metabolism
- Methylation
- Phosphorylation
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Species Specificity
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Sulfolobus acidocaldarius/genetics
- Sulfolobus acidocaldarius/metabolism
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Affiliation(s)
- F Kirpekar
- Department of Molecular Biology, Odense University, Denmark.
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182
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Massenet S, Ansmant I, Motorin Y, Branlant C. The first determination of pseudouridine residues in 23S ribosomal RNA from hyperthermophilic Archaea Sulfolobus acidocaldarius. FEBS Lett 1999; 462:94-100. [PMID: 10580099 DOI: 10.1016/s0014-5793(99)01524-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We describe the first identification of pseudouridine (Psi) residues in ribosomal RNA (23S rRNA) of an hyperthermophilic Archaea Sulfolobus acidocaldarius. In contrast to Eucarya rRNA, only six Psi residues were detected, which is rather close to the situation in Bacteria. However, three modified positions (Psi(2479), Psi(2535) and Psi(2550)) are unique for S. acidocaldarius. Two Psi residues at positions 2060 and 2594 are universally conserved, while one other Psi (position 2066) is also common to Eucarya. Taken together the results argue against the conservation of Psi-synthases between Archaea and Bacteria and provide a basis for the search of snoRNA-like guides for Psi formation in Archaea.
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Affiliation(s)
- S Massenet
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy I, Faculté des Sciences, P.O. Box 239, 54506, Vandoeuvre-les-Nancy, France
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183
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Abstract
The recognition manner of tRNA(Leu), a class II tRNA characterized by a long variable arm, by leucyl-tRNA synthetase from an extreme halophilic archaea, Haloferax volcanii, was studied using the in vitro transcription system. It was found that the discriminator base (A73) and the long variable arm, especially the specific loop sequence A47CG47D and U47H at the base of this helix, are significant for recognition by LeuRS. An appropriate stem length of the variable arm was also required. Base substitutions in the anticodon arm did not affect the leucylation activity. Transplantation of both the discriminator base and the variable arm of tRNA(Leu) was not sufficient to introduce leucylation activity to tRNA(Ser). Insertion of an additional nucleotide into the D-loop, which is not involved in the direct interaction with LeuRS, converted tRNA(Ser) to an efficient leucine acceptor. This suggests that differences in the tertiary structure play a key role in eliminating tRNA(Ser). The sequence-specific recognition of the long variable arm of tRNA(Leu) has not been observed in any of other organisms reported, such as Escherichia coli, yeast or human. On the other hand, the mode of discrimination from non-cognate tRNAs is similar to that in E. coli in that differences in the tertiary structure play a key role. Similarity extends to the substrate stringency, exemplified by a cross-species aminoacylation study showing that no class II tRNAs from E. coli or yeast can be leucylated by H. volcanii LeuRS. Our results have implications for the understanding of the evolution of the recognition system of class II tRNA.
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MESH Headings
- Acylation
- Anticodon/chemistry
- Anticodon/genetics
- Archaeal Proteins/chemistry
- Archaeal Proteins/metabolism
- Base Sequence
- Conserved Sequence/genetics
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Haloferax volcanii/enzymology
- Haloferax volcanii/genetics
- Kinetics
- Leucine/metabolism
- Leucine-tRNA Ligase/chemistry
- Leucine-tRNA Ligase/metabolism
- Mutation/genetics
- Nucleic Acid Conformation
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Transfer, Leu/chemistry
- RNA, Transfer, Leu/genetics
- RNA, Transfer, Leu/metabolism
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Substrate Specificity
- Transcription, Genetic/genetics
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Affiliation(s)
- A Soma
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, 036-8561, Japan
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184
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Ban N, Nissen P, Hansen J, Capel M, Moore PB, Steitz TA. Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit. Nature 1999; 400:841-7. [PMID: 10476961 DOI: 10.1038/23641] [Citation(s) in RCA: 310] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have calculated at 5.0 A resolution an electron-density map of the large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modification procedures. More than 300 base pairs of A-form RNA duplex have been fitted into this map, as have regions of non-A-form duplex, single-stranded segments and tetraloops. The long rods of RNA crisscrossing the subunit arise from the stacking of short, separate double helices, not all of which are A-form, and in many places proteins crosslink two or more of these rods. The polypeptide exit channel was marked by tungsten cluster compounds bound in one heavy-atom-derivatized crystal. We have determined the structure of the translation-factor-binding centre by fitting the crystal structures of the ribosomal proteins L6, L11 and L14, the sarcin-ricin loop RNA, and the RNA sequence that binds L11 into the electron density. We can position either elongation factor G or elongation factor Tu complexed with an aminoacylated transfer RNA and GTP onto the factor-binding centre in a manner that is consistent with results from biochemical and electron microscopy studies.
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Affiliation(s)
- N Ban
- Department of Molecular Biophysics & Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, Connecticut 06520-8114, USA
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185
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Hethke C, Bergerat A, Hausner W, Forterre P, Thomm M. Cell-free transcription at 95 degrees: thermostability of transcriptional components and DNA topology requirements of Pyrococcus transcription. Genetics 1999; 152:1325-33. [PMID: 10430563 PMCID: PMC1460703 DOI: 10.1093/genetics/152.4.1325] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cell-free transcription of archaeal promoters is mediated by two archaeal transcription factors, aTBP and TFB, which are orthologues of the eukaryotic transcription factors TBP and TFIIB. Using the cell-free transcription system described for the hyperthermophilic Archaeon Pyrococcus furiosus by Hethke et al., the temperature limits and template topology requirements of archaeal transcription were investigated. aTBP activity was not affected after incubation for 1 hr at 100 degrees. In contrast, the half-life of RNA polymerase activity was 23 min and that of TFB activity was 3 min. The half-life of a 328-nt RNA product was 10 min at 100 degrees. Best stability of RNA was observed at pH 6, at 400 mm K-glutamate in the absence of Mg(2+) ions. Physiological concentrations of K-glutamate were found to stabilize protein components in addition, indicating that salt is an important extrinsic factor contributing to thermostability. Both RNA and proteins were stabilized by the osmolyte betaine at a concentration of 1 m. The highest activity for RNA synthesis at 95 degrees was obtained in the presence of 1 m betaine and 400 mm K-glutamate. Positively supercoiled DNA, which was found to exist in Pyrococcus cells, can be transcribed in vitro both at 70 degrees and 90 degrees. However, negatively supercoiled DNA was the preferred template at all temperatures tested. Analyses of transcripts from plasmid topoisomers harboring the glutamate dehydrogenase promoter and of transcription reactions conducted in the presence of reverse gyrase indicate that positive supercoiling of DNA inhibits transcription from this promoter.
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MESH Headings
- Archaeal Proteins/metabolism
- Cell-Free System
- DNA Topoisomerases, Type I
- DNA Topoisomerases, Type II/metabolism
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA-Directed RNA Polymerases/metabolism
- Gene Expression Regulation, Archaeal
- Half-Life
- Hot Temperature
- Nucleic Acid Conformation
- Protein Denaturation
- Pyrococcus furiosus/genetics
- Pyrococcus furiosus/physiology
- RNA, Archaeal/biosynthesis
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Transcription, Genetic
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Affiliation(s)
- C Hethke
- Institut für Allgemeine Mikrobiologie, Universität Kiel, D-24118 Kiel, Germany
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186
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Abstract
A new type of structural compensation between the lengths of two perpendicularly oriented RNA double helices was found in the archaeal selenocysteine tRNA from Methanococcus jannascii. This tRNA contains only four base-pairs in the T-stem, one base-pair less than in all other cytosolic tRNAs. Our analysis shows that such a T-stem in an otherwise normal tRNA cannot guarantee the formation of the normal interactions between the D and T-loops. The absence of these interactions would affect the juxtaposition of the two tRNA helical domains, potentially damaging the tRNA function. In addition to the short T-stem, this tRNA possesses another unprecedented feature, a very long D-stem consisting of seven base-pairs. Taken as such, a seven base-pair D-stem will also disrupt the normal interaction between the D and T-loops. On the other hand, the presence of the universal nucleotides in both the D and T-loops suggests that these loops probably interact with each other in the same way as in other tRNAs. Here, we demonstrate that the short T-stem and the long D-stem can naturally compensate each other, thus providing the normal D/T interactions. Molecular modeling has helped suggest a detailed scheme of mutual compensation between these two unique structural aspects of the archaeal selenocysteine tRNA. In the light of this analysis, other structural and functional characteristics of the selenocysteine tRNAs are discussed.
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Affiliation(s)
- A Ioudovitch
- Département de Biochimie, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
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187
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Abstract
The RNA subunits of RNase Ps of Archaea and eukaryotes have been thought to depend fundamentally on protein for activity, unlike those of Bacteria that are capable of efficient catalysis in the absence of protein. Although the eukaryotic RNase P RNAs are quite different than those of Bacteria in both sequence and structure, the archaeal RNAs generally contain the sequences and structures of the bacterial, phylogenetically conserved catalytic core. A spectrum of archaeal RNase P RNAs were therefore tested for activity in a wide range of conditions. Many remain inactive in ionically extreme conditions, but catalytic activity could be detected from those of the methanobacteria, thermococci, and halobacteria. Chimeric holoenzymes, reconstituted from the Methanobacterium RNase P RNA and the Bacillus subtilis RNase P protein subunits, were functional at low ionic strength. The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterial RNase P protein) are similar to synthetic RNase P RNAs that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements.
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Affiliation(s)
- J A Pannucci
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA
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188
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Constantinesco F, Motorin Y, Grosjean H. Transfer RNA modification enzymes from Pyrococcus furiosus: detection of the enzymatic activities in vitro. Nucleic Acids Res 1999; 27:1308-15. [PMID: 9973619 PMCID: PMC148317 DOI: 10.1093/nar/27.5.1308] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The modification patterns of in vitro transcripts of two yeast Saccharomyces cerevisiae tRNAs (tRNAPheand tRNAAsp) and one archaeal Haloferax volcanii tRNA (tRNAIle) were investigated in the cell-free extract of Pyrococcus furiosus supplemented with S -adenosyl-l-methionine (AdoMet). The results indicate that the enzymatic formation of 11 distinct modified nucleotides corresponding to 12 enzymatic activities can be detected in vitro. They correspond to the formation of pseudouridines (Psi) at positions 39 and 55, 2' -O- ribose methylations at positions 6 (Am) and 56 (Cm), base methylations at positions 10 (m2G), 26 (m22G), 37 (m1G), 49 (m5C), 54 (m5U) and 58 (m1A) and both the deamination and methylation of adenosine into m1I at position 57. Most of the detected modified nucleotides are common modifications found in other phylogenetic groups, while Am6, Cm56and m1I57are specific modifications found exclusively in Archaea. It is also shown that the enzymatic formation of m5C49, m5U54, Psi55and m1I57does not depend on the three-dimensional architecture of the tRNA substrate, since these modi-fications also occur in fragmented tRNAs as substrate.
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MESH Headings
- Base Sequence
- Cell-Free System
- Molecular Sequence Data
- Nucleic Acid Conformation
- Pyrococcus furiosus/enzymology
- RNA, Archaeal/chemistry
- RNA, Archaeal/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Substrate Specificity
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- F Constantinesco
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique,1 Avenue de la Terrasse, Batiment 34, F-91198 Gif-sur-Yvette, France
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189
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Abstract
The G+C nucleotide content of ribosomal RNA (rRNA) sequences is strongly correlated with the optimal growth temperature of prokaryotes. This property allows inference of the environmental temperature of the common ancestor to all life forms from knowledge of the G+C content of its rRNA sequences. A model of sequence evolution, assuming varying G+C content among lineages and unequal substitution rates among sites, was devised to estimate ancestral base compositions. This method was applied to rRNA sequences of various species representing the major lineages of life. The inferred G+C content of the common ancestor to extant life forms appears incompatible with survival at high temperature. This finding challenges a widely accepted hypothesis about the origin of life.
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Affiliation(s)
- N Galtier
- Laboratoire de Biométrie, Génétique et Biologie des Populations, Université C. Bernard Lyon 1, France
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190
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Abstract
Ribonuclease P is responsible for the 5'-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria (and some Archaea) the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models and accessory information, available via the World Wide Web at the following URL: http://www.mbio.ncsu.edu/RNaseP/home .html
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MESH Headings
- Databases, Factual
- Endoribonucleases/chemistry
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- Eukaryotic Cells/chemistry
- Eukaryotic Cells/metabolism
- Information Storage and Retrieval
- Internet
- Models, Molecular
- Nucleic Acid Conformation
- Organelles/chemistry
- Organelles/genetics
- Organelles/metabolism
- Phylogeny
- Protein Structure, Secondary
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- Ribonuclease P
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Sequence Alignment
- Software
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Affiliation(s)
- J W Brown
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA.
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191
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Hasegawa Y, Sawaoka N, Kado N, Ochi M, Itoh T. Cloning and sequencing of the homologues of both the bacterial and eukaryotic initiation factor genes (hIF-2 and heIF-2 gamma) from archaeal Halobacterium halobium. Biochem Mol Biol Int 1998; 46:495-507. [PMID: 9818089 DOI: 10.1080/15216549800204022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The cloning and sequencing of the genes encoding the translational initiation factors (hIF-2 and heIF-2 gamma) was performed by screening the halophilic archaeon Halobacterium halobium genomic library with a probe constructed from the peptide IGHVDHGK that is conserved in archaeal GTP-binding elongation factors. The codon usage by the hIF-2 and heIF-2 gamma genes showed a preference for triplets ending in G or C. This characteristic is almost identical to that of other H. halobium genes. The translated protein of hIF-2 and heIF-2 gamma genes is made of 414 and 583 amino acid residues, respectively, and contains the sequence motif for the binding of GTP. The sequence of hIF-2 shows a strong similarity to the initiation factor IF-2 from Bacteria whereas heIF-2 gamma shows a strong similarity to the initiation factor eIF-2 gamma from Eucarya.
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Affiliation(s)
- Y Hasegawa
- Department of Bioresource Development, Hiroshima Prefectural University, Japan
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192
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Hubert N, Sturchler C, Westhof E, Carbon P, Krol A. The 9/4 secondary structure of eukaryotic selenocysteine tRNA: more pieces of evidence. RNA 1998; 4:1029-33. [PMID: 9740122 PMCID: PMC1369679 DOI: 10.1017/s1355838298980888] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
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193
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Abstract
Soda lakes are highly alkaline extreme environments that form in closed drainage basins exposed to high evaporation rates. Because of the scarcity of Mg2+ and Ca2+ in the water chemistry, the lakes become enriched in CO3(2-) and Cl-, with pHs in the range 8 to > 12. Although there is a clear difference in prokaryotic communities between the hypersaline lakes where NaCl concentrations are > 15% w/v and more dilute waters, i.e., NaCl concentrations about 5% w/v, photosynthetic primary production appears to be the basis of all nutrient recycling. In both the aerobic and anaerobic microbial communities the major trophic groups responsible for cycling of carbon and sulfur have in general been identified. Systematic studies have shown that the microbes are alkaliphilic and many represent separate lineages within accepted taxa, while others show no strong relationship to known prokaryotes. Although alkaliphiles are widespread it seems probable that these organisms, especially those unique to the hypersaline lakes, evolved separately within an alkaline environment. Although present-day soda lakes are geologically quite recent, they have probably existed since archaean times, permitting the evolution of independent communities of alkaliphiles since an early period in the Earth's history.
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MESH Headings
- Archaea/genetics
- Archaea/isolation & purification
- Archaea/metabolism
- Bacteria, Aerobic/genetics
- Bacteria, Aerobic/isolation & purification
- Bacteria, Aerobic/metabolism
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/isolation & purification
- Bacteria, Anaerobic/metabolism
- Base Sequence
- Biological Evolution
- Environment
- Fresh Water/microbiology
- Hydrogen-Ion Concentration
- Models, Biological
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
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Affiliation(s)
- B E Jones
- Genencor International BV, Delft, The Netherlands.
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194
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Ban N, Freeborn B, Nissen P, Penczek P, Grassucci RA, Sweet R, Frank J, Moore PB, Steitz TA. A 9 A resolution X-ray crystallographic map of the large ribosomal subunit. Cell 1998; 93:1105-15. [PMID: 9657144 DOI: 10.1016/s0092-8674(00)81455-5] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The 50S subunit of the ribosome catalyzes the peptidyl-transferase reaction of protein synthesis. We have generated X-ray crystallographic electron density maps of the large ribosomal subunit from Haloarcula marismortui at various resolutions up to 9 A using data from crystals that diffract to 3 A. Positioning a 20 A resolution EM image of these particles in the crystal lattice produced phases accurate enough to locate the bound heavy atoms in three derivatives using difference Fourier maps, thus demonstrating the correctness of the EM model and its placement in the unit cell. At 20 A resolution, the X-ray map is similar to the EM map; however, at 9 A it reveals long, continuous, but branched features whose shape, diameter, and right-handed twist are consistent with segments of double-helical RNA that crisscross the subunit.
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Affiliation(s)
- N Ban
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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195
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Diener JL, Moore PB. Solution structure of a substrate for the archaeal pre-tRNA splicing endonucleases: the bulge-helix-bulge motif. Mol Cell 1998; 1:883-94. [PMID: 9660971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The structure of the bulge-helix-bulge motif that constitutes the intron/exon splice site in H. volcanii pre-tRNATrp has been determined by NMR spectroscopy. The conformations of the two 3 nt bulges, where the pre-tRNA is cleaved, are stabilized by stacking interactions between bulge nucleotides and bases in the adjacent Watson-Crick helices and by a network of backbone hydrogen bonds. Both bulges are presented on the same minor groove face of the central 4 bp helix, and the overall structure has approximate two-fold symmetry, which makes it well-suited for attack by archaeal splicing endonucleases, which are symmetric dimers.
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Affiliation(s)
- J L Diener
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
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196
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Fabbri S, Fruscoloni P, Bufardeci E, Di Nicola Negri E, Baldi MI, Attardi DG, Mattoccia E, Tocchini-Valentini GP. Conservation of substrate recognition mechanisms by tRNA splicing endonucleases. Science 1998; 280:284-6. [PMID: 9535657 DOI: 10.1126/science.280.5361.284] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Accuracy in transfer RNA (tRNA) splicing is essential for the formation of functional tRNAs, and hence for gene expression, in both Eukaryotes and Archaea. The specificity for recognition of the tRNA precursor (pre-tRNA) resides in the endonuclease, which removes the intron by making two independent endonucleolytic cleavages. Although the eukaryal and archaeal enzymes appear to use different features of pre-tRNAs to determine the sites of cleavage, analysis of hybrid pre-tRNA substrates containing eukaryal and archaeal sequences, described here, reveals that the eukaryal enzyme retains the ability to use the archaeal recognition signals. This result indicates that there may be a common ancestral mechanism for recognition of pre-tRNA by proteins.
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Affiliation(s)
- S Fabbri
- EniChem, Istituto Guido Donegani SpA, Laboratori di Biotecnologie, 00015 Monterotondo, Rome, Italy
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197
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Abstract
The splicing of transfer RNA precursors is similar in Eucarya and Archaea. In both kingdoms an endonuclease recognizes the splice sites and releases the intron, but the mechanism of splice site recognition is different in each kingdom. The crystal structure of the endonuclease from the archaeon Methanococcus jannaschii was determined to a resolution of 2.3 angstroms. The structure indicates that the cleavage reaction is similar to that of ribonuclease A and the arrangement of the active sites is conserved between the archaeal and eucaryal enzymes. These results suggest an evolutionary pathway for splice site recognition.
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Affiliation(s)
- H Li
- Division of Biology, Mail Code 147-75, California Institute of Technology, Pasadena, CA 91125, USA
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198
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Abstract
Phylogenetic analyses of archaeal 16S rRNA genes (rDNA) from DNA extracted from continental shelf sediments revealed the presence of two major lineages, belonging to the kingdoms Crenarchaeota and Euryarchacota, respectively. Our analyses indicate that the benthic Archaea belong to a new group, divergent from the marine low-temperature planktonic Archaea. This is the first report showing the existence of Archaea, unrelated to methanogens, specifically associated with low-temperature anoxic marine sediments.
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Affiliation(s)
- C Vetriani
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore 21202, USA.
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199
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Cann IK, Ishino Y. A tRNA(Glu) gene from the hyperthermophilic archaeon Pyrococcus furiosus contains the 3'-terminal CCA sequence of the mature tRNA. FEMS Microbiol Lett 1998; 160:199-204. [PMID: 9532738 DOI: 10.1111/j.1574-6968.1998.tb12911.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We cloned a gene encoding tRNA(Glu) of the hyperthermophilic archaeon Pyrococcus furiosus. This gene contains the CCA sequence corresponding to the 3'-terminus of the mature tRNA. It is known that, like in eukaryal tRNAs, the CCA-termini of archaeal tRNAs are generally not encoded. Therefore, we analyzed all tRNA genes in the genome of Methanococcus jannaschii estimated by its whole genome sequence. Twenty-one of 37 listed tRNA genes contained the 3'-terminal CCA sequence. The corresponding M. jannaschii tRNA(Glu) gene does not contain the CCA sequence, although the tRNA sequences of the M. jannaschii and P. furiosus tRNA(Glu) genes are 86% identical.
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Affiliation(s)
- I K Cann
- Department of Molecular Biology, Biomolecular Engineering Research Institute, Osaka, Japan
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200
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Briganti G, Giordano R, Londei P, Pedone F. Small angle neutron scattering analysis of thermal stability of 23S rRNA and the intact 50S subunits of Sulfolobus solfataricus. Biochim Biophys Acta 1998; 1379:297-301. [PMID: 9528666 DOI: 10.1016/s0304-4165(97)00066-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ribosomes of the extremely thermophilic archaebacterium, Sulfolobus solfataricus, are very resistant to thermal denaturation (optimal growth temperature 87 degrees C), remaining essentially intact up to above 90 degrees C. However, the separate ribosomal components (rRNA and r-proteins) are less thermally stable than the ribosome as a whole, indicating that the mode of interaction of all of the components within the ribonucleoprotein particle play an essential role in determining thermal stability. To get some insight into the structural features of the thermophilic ribosome, we performed small angle neutron scattering (SANS) measurements at various temperatures on Sulfolobus solfataricus intact large ribosomal subunits (50S) and deproteinated large ribosomal subunit RNA (23S). Even if the scattering profiles suggest the presence of supramolecular aggregates in all of the samples and at all of the investigated temperatures, the measured form factors indicated for both samples that, at temperatures above 70 degrees C, the suspended particles underwent a structural rearrangement. This finding is likely to reflect single particles' properties, since S. solfataricus ribosomes are known to be biologically activated only above 60 degrees C, and there are indications that such activation requires a conformational rearrangement of the particle. A remarkable superimposition of the percentage variation of the volume from neutron scattering and of the absorbency increment with respect to temperature supports this view.
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Affiliation(s)
- G Briganti
- INFM Department of Physics, University La Sapienza, Rome, Italy.
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