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Welty R, Pabit SA, Katz AM, Calvey GD, Pollack L, Hall KB. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure. RNA (NEW YORK, N.Y.) 2018; 24:1828-1838. [PMID: 30254137 PMCID: PMC6239185 DOI: 10.1261/rna.068361.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 05/22/2023]
Abstract
Folding of an RNA from secondary to tertiary structure often depends on divalent ions for efficient electrostatic charge screening (nonspecific association) or binding (specific association). To measure how different divalent cations modify folding kinetics of the 60 nucleotide Ecoli rRNA GTPase center, we combined stopped-flow fluorescence in the presence of Mg2+, Ca2+, or Sr2+ together with time-resolved small angle X-ray scattering (SAXS) in the presence of Mg2+ to observe the folding process. Immediately upon addition of each divalent ion, the RNA undergoes a transition from an extended state with secondary structure to a more compact structure. Subsequently, specific divalent ions modulate populations of intermediates in conformational ensembles along the folding pathway with transition times longer than 10 msec. Rate constants for the five folding transitions act on timescales from submillisecond to tens of seconds. The sensitivity of RNA tertiary structure to divalent cation identity affects all but the fastest events in RNA folding, and allowed us to identify those states that prefer Mg2+ The GTPase center RNA appears to have optimized its folding trajectory to specifically utilize this most abundant intracellular divalent ion.
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Affiliation(s)
- Robb Welty
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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2
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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3
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Dumesic PA, Rosenblad MA, Samuelsson T, Nguyen T, Moresco JJ, Yates JR, Madhani HD. Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Res 2015; 43:9017-27. [PMID: 26275773 PMCID: PMC4605306 DOI: 10.1093/nar/gkv819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 08/01/2015] [Indexed: 12/21/2022] Open
Abstract
Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features-SRP RNA helix 8 and Srp54-in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Magnus A Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tiffany Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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Havrila M, Réblová K, Zirbel CL, Leontis NB, Šponer J. Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop. J Phys Chem B 2013; 117:14302-19. [PMID: 24144333 PMCID: PMC3946555 DOI: 10.1021/jp408530w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with a highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Nonisosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. The MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that the inability to form stable cWW geometry is an important factor in the case of the first base pair of the flexible region of the SR motif. A comparison of structural, bioinformatics, SHAPE probing, and MD simulation data reveals that explicit solvent MD simulations neatly reflect the viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions.
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Affiliation(s)
- Marek Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Craig L. Zirbel
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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Zhang HL, Huang Y, Lin LL, Wang XY, Zheng ZM. The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences. Zool Stud 2013. [DOI: 10.1186/1810-522x-52-37] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The phylogeny of the Orthoptera was analyzed based on 6 datasets from 47 orthopteran mitochondrial genomes (mitogenomes). The phylogenetic signals in the mitogenomes were rigorously examined under analytical regimens of maximum likelihood (ML) and Bayesian inference (BI), along with how gene types and different partitioning schemes influenced the phylogenetic reconstruction within the Orthoptera. The monophyly of the Orthoptera and its two suborders (Caelifera and Ensifera) was consistently recovered in the analyses based on most of the datasets we selected, regardless of the optimality criteria.
Results
When the seven NADH dehydrogenase subunits were concatenated into a single alignment (NADH) and were analyzed; a near-identical topology to the traditional morphological analysis was recovered, especially for BI_NADH. In both the concatenated cytochrome oxidase (COX) subunits and COX + cytochrome b (Cyt b) datasets, the small extent of sequence divergence seemed to be helpful for resolving relationships among major Orthoptera lineages (between suborders or among superfamilies). The conserved and variable domains of ribosomal (r)RNAs performed poorly when respectively analyzed but provided signals at some taxonomic levels.
Conclusions
Our findings suggest that the best phylogenetic inferences can be made when moderately divergent nucleotide data from mitogenomes are analyzed, and that the NADH dataset was suited for studying orthopteran phylogenetic relationships at different taxonomic levels, which may have been due to the larger amount of DNA sequence data and the larger number of phylogenetically informative sites.
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Zhao YE, Wang ZH, Xu Y, Wu LP, Hu L. Secondary structure prediction for complete rDNA sequences (18S, 5.8S, and 28S rDNA) of Demodex folliculorum, and comparison of divergent domains structures across Acari. Exp Parasitol 2013; 135:370-81. [DOI: 10.1016/j.exppara.2013.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 05/06/2013] [Accepted: 07/31/2013] [Indexed: 11/24/2022]
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Das A, Ghosh J, Bhattacharya A, Samanta D, Das D, Das Gupta C. Involvement of mitochondrial ribosomal proteins in ribosomal RNA-mediated protein folding. J Biol Chem 2011; 286:43771-43781. [PMID: 22020935 DOI: 10.1074/jbc.m111.263574] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The peptidyl transferase center of the domain V of large ribosomal RNA in the prokaryotic and eukaryotic cytosolic ribosomes acts as general protein folding modulator. We showed earlier that one part of the domain V (RNA1 containing the peptidyl transferase loop) binds unfolded protein and directs it to a folding competent state (FCS) that is released by the other part (RNA2) to attain the folded native state by itself. Here we show that the peptidyl transferase loop of the mitochondrial ribosome releases unfolded proteins in FCS extremely slowly despite its lack of the rRNA segment analogous to RNA2. The release of FCS can be hastened by the equivalent activity of RNA2 or the large subunit proteins of the mitochondrial ribosome. The RNA2 or large subunit proteins probably introduce some allosteric change in the peptidyl transferase loop to enable it to release proteins in FCS.
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Affiliation(s)
- Anindita Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India; Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, Nadia 741252, India
| | - Jaydip Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India; Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Arpita Bhattacharya
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India
| | - Dibyendu Samanta
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India
| | - Debasis Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India
| | - Chanchal Das Gupta
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India; Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, Nadia 741252, India.
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Yilmaz P, Kottmann R, Pruesse E, Quast C, Glöckner FO. Analysis of 23S rRNA genes in metagenomes – A case study from the Global Ocean Sampling Expedition. Syst Appl Microbiol 2011; 34:462-9. [DOI: 10.1016/j.syapm.2011.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/04/2011] [Accepted: 04/04/2011] [Indexed: 12/19/2022]
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Lancaster L, Lambert NJ, Maklan EJ, Horan LH, Noller HF. The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit. RNA (NEW YORK, N.Y.) 2008; 14:1999-2012. [PMID: 18755834 PMCID: PMC2553751 DOI: 10.1261/rna.1202108] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The sarcin-ricin loop (SRL) of 23S rRNA in the large ribosomal subunit is a factor-binding site that is essential for GTP-catalyzed steps in translation, but its precise functional role is thus far unknown. Here, we replaced the 15-nucleotide SRL with a GAAA tetraloop and affinity purified the mutant 50S subunits for functional and structural analysis in vitro. The SRL deletion caused defects in elongation-factor-dependent steps of translation and, unexpectedly, loss of EF-Tu-independent A-site tRNA binding. Detailed chemical probing analysis showed disruption of a network of rRNA tertiary interactions that hold together the 23S rRNA elements of the functional core of the 50S subunit, accompanied by loss of ribosomal protein L16. Our results reveal an influence of the SRL on the higher-order structure of the 50S subunit, with implications for its role in translation.
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Affiliation(s)
- Laura Lancaster
- Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR. Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. INSECT MOLECULAR BIOLOGY 2006; 15:657-86. [PMID: 17069639 PMCID: PMC2048585 DOI: 10.1111/j.1365-2583.2006.00689.x] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/28/2006] [Indexed: 05/12/2023]
Abstract
As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.
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Affiliation(s)
- J J Gillespie
- Department of Entomology, Texas A & M University, College Station, TX, USA.
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MANGANELLI GIUSEPPE, SALOMONE NICOLA, GIUSTI FOLCO. A molecular approach to the phylogenetic relationships of the western palaearctic Helicoidea (Gastropoda: Stylommatophora). Biol J Linn Soc Lond 2005. [DOI: 10.1111/j.1095-8312.2005.00514.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Gillespie JJ, Munro JB, Heraty JM, Yoder MJ, Owen AK, Carmichael AE. A Secondary Structural Model of the 28S rRNA Expansion Segments D2 and D3 for Chalcidoid Wasps (Hymenoptera: Chalcidoidea). Mol Biol Evol 2005; 22:1593-608. [PMID: 15843598 DOI: 10.1093/molbev/msi152] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyze the secondary structure of two expansion segments (D2, D3) of the 28S ribosomal (rRNA)-encoding gene region from 527 chalcidoid wasp taxa (Hymenoptera: Chalcidoidea) representing 18 of the 19 extant families. The sequences are compared in a multiple sequence alignment, with secondary structure inferred primarily from the evidence of compensatory base changes in conserved helices of the rRNA molecules. This covariation analysis yielded 36 helices that are composed of base pairs exhibiting positional covariation. Several additional regions are also involved in hydrogen bonding, and they form highly variable base-pairing patterns across the alignment. These are identified as regions of expansion and contraction or regions of slipped-strand compensation. Additionally, 31 single-stranded locales are characterized as regions of ambiguous alignment based on the difficulty in assigning positional homology in the presence of multiple adjacent indels. Based on comparative analysis of these sequences, the largest genetic study on any hymenopteran group to date, we report an annotated secondary structural model for the D2, D3 expansion segments that will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related apocritan taxa.
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13
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14
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Gillespie J, Cannone J, Gutell R, Cognato A. A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae). INSECT MOLECULAR BIOLOGY 2004; 13:495-518. [PMID: 15373807 DOI: 10.1111/j.0962-1075.2004.00509.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We analysed the secondary structure of two expansion segments (D2, D3) of the 28S rRNA gene from 229 leaf beetles (Coleoptera: Chrysomelidae), the majority of which are in the subfamily Galerucinae. The sequences were compared in a multiple sequence alignment, with secondary structure inferred primarily from the compensatory base changes in the conserved helices of the rRNA molecules. This comparative approach yielded thirty helices comprised of base pairs with positional covariation. Based on these leaf beetle sequences, we report an annotated secondary structural model for the D2 and D3 expansion segments that will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related beetle taxa. This predicted structure, consisting of seven major compound helices, is mostly consistent with previously proposed models for the D2 and D3 expansion segments in insects. Despite a lack of conservation in the primary structure of these regions of insect 28S rRNA, the evolution of the secondary structure of these seven major motifs may be informative above the nucleotide level for higher-order phylogeny reconstruction of major insect lineages.
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Affiliation(s)
- J Gillespie
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA.
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15
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Abstract
The lonepair triloop (LPTL) is an RNA structural motif that contains a single ("lone") base-pair capped by a hairpin loop containing three nucleotides. The two nucleotides immediately outside of this motif (5' and 3' to the lonepair) are not base-paired to one another, restricting the length of this helix to a single base-pair. Four examples of this motif, along with three tentative examples, were initially identified in the 16S and 23S rRNAs with covariation analysis. An evaluation of the recently determined crystal structures of the Thermus thermophilus 30S and Haloarcula marismortui 50S ribosomal subunits revealed the authenticity for all of these proposed interactions and identified 16 more LPTLs in the 5S, 16S and 23S rRNAs. This motif is found in the T loop in the tRNA crystal structures. The lonepairs are positioned, in nearly all examples, immediately 3' to a regular secondary structure helix and are stabilized by coaxial stacking onto this flanking helix. In all but two cases, the nucleotides in the triloop are involved in a tertiary interaction with another section of the rRNA, establishing an overall three-dimensional function for this motif. Of these 24 examples, 14 occur in multi-stem loops, seven in hairpin loops and three in internal loops. While the most common lonepair, U:A, occurs in ten of the 24 LPTLs, the remaining 14 LPTLs contain seven different base-pair types. Only a few of these lonepairs adopt the standard Watson-Crick base-pair conformations, while the majority of the base-pairs have non-standard conformations. While the general three-dimensional conformation is similar for all examples of this motif, characteristic differences lead to several subtypes present in different structural environments. At least one triloop nucleotide in 22 of the 24 LPTLs in the rRNAs and tRNAs forms a tertiary interaction with another part of the RNA. When a LPTL containing the GNR or UYR triloop sequence forms a tertiary interaction with the first (and second) triloop nucleotide, it recruits a fourth nucleotide to mediate stacking and mimic the tetraloop conformation. Approximately half of the LPTL motifs are in close association with proteins. The majority of these LPTLs are positioned at sites in rRNAs that are conserved in the three phylogenetic domains; a few of these occur in regions of the rRNA associated with ribosomal function, including the presumed site of peptidyl transferase activity in the 23S rRNA.
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Affiliation(s)
- Jung C Lee
- The University of Texas at Austin, College of Pharmacy, 1 University Station, A1900, Austin, TX 78712-0120, USA
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16
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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] [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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17
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Abstract
The aminoacyl (A site) tRNA analog 4-thio-dT-p-C-p-puromycin (s4TCPm) photochemically cross-links with high efficiency and specificity to G2553 of 23S rRNA and is peptidyl transferase reactive in its cross-linked state, establishing proximity between the highly conserved 2555 loop in domain V of 23S rRNA and the universally conserved CCA end of tRNA. To test for base-pairing interactions between 23S rRNA and aminoacyl tRNA, site-directed mutations were made at the universally conserved nucleotides U2552 and G2553 of 23S rRNA in both E. coli and B. stearothermophilus ribosomal RNA and incorporated into ribosomes. Mutations at G2553 resulted in dominant growth defects in E. coli and in decreased levels of peptidyl transferase activity in vitro. Genetic analysis in vitro of U2552 and G2553 mutant ribosomes and CCA end mutant tRNA substrates identified a base-pairing interaction between C75 of aminoacyl tRNA and G2553 of 23S rRNA.
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MESH Headings
- 2-Aminopurine/analogs & derivatives
- 2-Aminopurine/chemistry
- 2-Aminopurine/metabolism
- Base Pairing/genetics
- Binding Sites
- Conserved Sequence/genetics
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Genes, Bacterial/genetics
- Geobacillus stearothermophilus/enzymology
- Geobacillus stearothermophilus/genetics
- Hydrogen Bonding
- Kinetics
- Mutagenesis, Site-Directed/genetics
- Mutation/genetics
- Nucleic Acid Conformation
- Peptidyl Transferases/chemistry
- Peptidyl Transferases/genetics
- Peptidyl Transferases/metabolism
- Puromycin/analogs & derivatives
- Puromycin/chemistry
- Puromycin/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Suppression, Genetic/genetics
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Affiliation(s)
- D F Kim
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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18
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Abstract
Atomic resolution structures are now available for more than 20 complexes of proteins with specific RNAs. This review examines two main themes that appear in this set of structures. A "groove binder" class of proteins places a protein structure (alpha-helix, 310-helix, beta-ribbon, or irregular loop) in the groove of an RNA helix, recognizing both the specific sequence of bases and the shape or dimensions of the groove, which are sometimes distorted from the normal A-form. A second class of proteins uses beta-sheet surfaces to create pockets that examine single-stranded RNA bases. Some of these proteins recognize completely unstructured RNA, and in others RNA secondary structure indirectly promotes binding by constraining bases in an appropriate orientation. Thermodynamic studies have shown that binding specificity is generally a function of several factors, including base-specific hydrogen bonds, non-polar contacts, and mutual accommodation of the protein and RNA-binding surfaces. The recognition strategies and structural frameworks used by RNA binding proteins are not exotically different from those employed by DNA-binding proteins, suggesting that the two kinds of nucleic acid-binding proteins have not evolved independently.
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Affiliation(s)
- D E Draper
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
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19
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Stepien CA, Hubers AN, Skidmore JL. Diagnostic genetic markers and evolutionary relationships among invasive dreissenoid and corbiculoid bivalves in North America: phylogenetic signal from mitochondrial 16S rDNA. Mol Phylogenet Evol 1999; 13:31-49. [PMID: 10508537 DOI: 10.1006/mpev.1999.0666] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Diagnostic genetic markers from 486 aligned nucleotide sequences of mitochondrial 16S ribosomal DNA were developed for the four closely related species of dreissenoid and corbiculoid bivalves that have invaded North America; the zebra mussel Dreissena polymorpha, the quagga mussel D. bugensis, and the dark false mussel Mytilopsis leucophaeata of the superfamily Dreissenoidea, and the Asian clam Corbicula fluminea of the sister superfamily Corbiculoidea. Evolutionary relationships were examined among the four genera and comparisons were made with native Eurasian populations of D. polymorpha and D. bugensis. Tests were conducted for gender-specific mitochondrial lineages, which occur in some other bivalves. Genetic variability and divergence rates were tested between stem (paired) and loop (unpaired) regions of secondary structure. There were 251 variable nucleotide sites, of which 99 were phylogenetically informative. Overall transition to transversion ratio was 0.76:1.00 and both accumulated linearly in stem and loop regions, suggesting appropriate phylogenetic signal. Genetic distance calibration with the fossil record estimated the pairwise sequence divergence as 0. 0057 +/- 0.0004 per million years. Mytilopsis and Dreissena appear to have diverged about 20.7 +/- 2.7 million years ago. D. bugensis and D. polymorpha appear separated by about 13.2 +/- 2.2 million years. No intraspecific variation was found, including between Eurasian and North American populations, among shallow and deep morphotypes of D. bugensis and between the sexes. Restriction endonuclease markers were developed to distinguish among the species at all life history stages, allowing rapid identification in areas of sympatric distribution.
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Affiliation(s)
- C A Stepien
- Department of Biology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-7080, USA.
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20
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Cheung J, Lin A. Probing surface structure of sarcin domain on ribosomes of Escherichia coli by complementary oligo DNAs and ribosome-inactivating protein. J Biomed Sci 1999; 6:277-84. [PMID: 10420085 DOI: 10.1007/bf02253569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The regional structure of the sarcin domain of 23S rRNA of Escherichia coli ribosomes was determined by a combinatory approach of oligo DNA probes and the action of alpha-sarcin. The sarcin domain is protected by a reactive complementary oligo DNA probe against the hydrolytic action of alpha-sarcin. This protective effect is dependent upon the length and the complementary sequence of oligo DNA probes that react to ribosomes. Under UV irradiation and using of the primer extension, nucleotides that contacted by reactive oligo DNA probes were determined. Nucleotides at the 3' side of the domain (positions from G2659 to C2676) were targeted by oligo DNA probes that have their sequences to complement the domain, indicating that the 3' side region was exposed on the surface of ribosomes, whereas nucleotides at the 5' side of stem and extented to two bases at the loop (positions from C2646 to A2654) were not accessible to any oligo DNA probes, implying that the region could be buried in ribosomes. This study also provided evidence that the conformation of the sarcin domain is subjected to alteration if the exposed 3' side of domain is targeted by the reactive DNA probe. The importance of the topological arrangement of the sarcin domain that engages in the translocation event during translation is discussed.
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Affiliation(s)
- J Cheung
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, ROC
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21
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Lacadena J, Martínez del Pozo A, Lacadena V, Martínez-Ruiz A, Mancheño JM, Oñaderra M, Gavilanes JG. The cytotoxin alpha-sarcin behaves as a cyclizing ribonuclease. FEBS Lett 1998; 424:46-8. [PMID: 9580156 DOI: 10.1016/s0014-5793(98)00137-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The hydrolysis of adenylyl(3'-->5')adenosine (ApA) and guanylyl(3'--> 5')adenosine (GpA) dinucleotides by the cytotoxic protein alpha-sarcin has been studied. Quantitative analysis of the reaction has been performed through reverse-phase chromatographic (HPLC) separation of the resulting products. The hydrolysis of the 3'-5' phosphodiester bond of these substrates yields the 2'-3' cyclic mononucleotide; this intermediate is converted into the corresponding 3'-monophosphate derivative as the final product of the reaction. The values of the apparent Michaelis constant (KM), kcat and kcat/KM have also been calculated. The obtained results fit into a two-step mechanism for the enzymatic activity of alpha-sarcin and allow to consider this protein as a cyclizing RNase.
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Affiliation(s)
- J Lacadena
- Departamento de Bioquímica y Biología Molecular I, Facultad de Química, Universidad Complutense de Madrid, Spain
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22
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Bukhman YV, Draper DE. Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure. J Mol Biol 1997; 273:1020-31. [PMID: 9367788 DOI: 10.1006/jmbi.1997.1383] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A 58 nucleotide fragment of Escherichia coli large subunit ribosomal RNA, nucleotides 1051 to 1108, adopts a specific tertiary structure normally requiring both monovalent (NH4+ or K+) and divalent (Mg2+) ions to fold; this ion-dependent structure is a prerequisite for recognition by ribosomal protein L11. Melting experiments have been used to show that a sequence variant of this fragment, GACG RNA, is able to adopt a stable tertiary structure in the presence of 1.6 M NH4Cl and absence of divalent ions. The similarity of this high-salt structure to the tertiary structure formed under more typical salt conditions (0.1 M NH4Cl and several mM MgCl2) was shown by its following properties: (i) an unusual ratio of hyperchromicity at 260 nm and 280 nm upon unfolding, (ii) selectivity for NH4+ over K+ or Na+, (iii) stabilization by L11 protein, and (iv) further stabilization by added Mg2+. Delocalized electrostatic interactions of divalent ions with nucleic acids should be very weak in the presence of >1 M monovalent salt; thus stabilization of the tertiary structure by low (<1 mM) Mg2+ concentrations in these high-salt conditions suggests that Mg2+ binds at specific site(s). GACG RNA tertiary structure unfolding in 1.6 M NH4Cl (Tm approximately 39 degrees C) is distinct from melting of the secondary structure (centered at approximately 72 degrees C), and it has been possible to calculate the free energy of tertiary structure stabilization upon addition of various divalent cations. From these binding free energies, ion-RNA binding isotherms for Mn2+, Mg2+, Ca2+, Sr2+ and Ba2+ have been obtained. All of these ions bind at two sites: one site favors Mg2+ and Ba2+ and discriminates against Ca2+, while the other site favors binding of smaller ions over larger ones (Mg2+ >Ca2+ >Sr2+ >Ba2+). Weak cooperative or anticooperative interactions between the sites, also dependent on ion radius, may also be taking place.
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Affiliation(s)
- Y V Bukhman
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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23
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Sapag A, Draper DE. In vitro evolution used to define a protein recognition site within a large RNA domain. Bioorg Med Chem 1997; 5:1097-105. [PMID: 9222503 DOI: 10.1016/s0968-0896(97)00045-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A minimum of 460 nucleotides of 16S ribosomal RNA are needed to fold the target site for E. coli ribosomal protein S4, although a much smaller region within this large domain is protected from chemical reagents by the protein. Starting with a 531-nucleotide tRNA fragment, cycles of mutagenesis, selection with S4, and amplification ('in vitro evolution') were used to obtain a pool of 30 RNA sequences selected for S4 recognition but approximately 30% different from wild type. Numerous compensatory base pair changes have largely preserved the same secondary structure among these RNAs as found in wild-type sequences. A 20-base deletion and a single nucleotide insertion are among several unusual features found in most of the selected sequences and also prevalent among other prokaryotic rRNAs. Most of the compensatory base changes and selected features are located outside of the region protected by S4 from chemical reagents. It was unexpected that S4 would select for RNA structures throughout such a large domain; the selected features are probably contributing indirectly to S4 recognition by promoting correct tertiary folding of the region actually contacted by S4. The role of S4 may be to stabilize this domain (nearly one-third of the 16S rRNA) in its proper conformation for ribosome function.
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MESH Headings
- Base Sequence
- Binding Sites
- Cloning, Molecular
- DNA, Complementary/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Evolution, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- Polymerase Chain Reaction
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Transcription, Genetic
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Affiliation(s)
- A Sapag
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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24
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Ofengand J, Bakin A. Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J Mol Biol 1997; 266:246-68. [PMID: 9047361 DOI: 10.1006/jmbi.1996.0737] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The pseudouridine (psi) residues present in the high molecular mass RNA from the large ribosomal subunit (LSU) have been sequenced from representative species of the eukaryotes, prokaryotes and archaebacteria, and from mitochondrial and chloroplast organelles. Ribosomes from Bacillus subtilis, Halobacter halobium, Drosphilia melanogaster, Mus musculus, Homo sapiens, mitochondria of M. musculus, H. sapiens and Trypanosoma brucei, and Zea mays chloroplasts were examined, resulting in the exact localization of 190 psi residues. The number of psi residues per RNA varied from one in the mitochondrial RNAs to 57 in the cytoplasmic LSU RNA of D. melanogaster and M. musculus. Despite this, all of the psi residues were found in three domains, II, IV and V. All three are at or have been linked to the peptidyl transferase center according to the literature. Comparison of the sites for psi among the species examined revealed four conserved or semi-conserved segments. One is the region 1911 to 1917, which contains three psi or modified psi in almost all species examined. This site is also juxtaposed to the decoding site of the 30 S subunit in the 70 S ribosome and has been implicated in the fidelity of codon recognition. Three additional sites were at the peptidyl transferase center itself. The juxtaposition of the conserved sites for psi with the two important functions of the ribosome, codon recognition and peptide bond formation, implies an important role for psi in ribosome function. We report some new putative modified nucleosides in LSU RNAs as detected by reverse transcription, correct a segment of the sequence of Z. mays chloroplasts and D. melanogaster LSU RNA, correlate the secondary structural context for all known psi residues in ribosomal RNA, and compare the sites for psi with those known for methylated nucleosides in H. sapiens.
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Affiliation(s)
- J Ofengand
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, FL 33101, USA
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25
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Xing Y, Guha Thakurta D, Draper DE. The RNA binding domain of ribosomal protein L11 is structurally similar to homeodomains. NATURE STRUCTURAL BIOLOGY 1997; 4:24-7. [PMID: 8989317 DOI: 10.1038/nsb0197-24] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The RNA binding domain of ribosomal protein L11 is strikingly similar to the homeodomain class of eukaryotic DNA binding proteins: it contains three alpha-helices that superimpose with homeodomain alpha-helices, and some conserved residues required for rRNA recognition align with homeodomain helix III residues contacting DNA bases.
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26
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Affiliation(s)
- S Limmer
- Laboratorium für Biochemie der Universität Bayreuth, Germany
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27
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Lydeard C, Mulvey M, Davis GM. Molecular systematics and evolution of reproductive traits of North American freshwater unionacean mussels (Mollusca: Bivalvia) as inferred from 16S rRNA gene sequences. Philos Trans R Soc Lond B Biol Sci 1996; 351:1593-603. [PMID: 9053909 DOI: 10.1098/rstb.1996.0143] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
North American freshwater unionacean bivalves are a diverse group of nearly 300 species. Unionaceans exhibit an array of conchological, anatomical, life history, and reproductive characteristics that have figured prominently in proposed classification schemes. Recently, two very different classifications of North American unionaceans have been proposed. Depending on the classification system utilized, a very different evolutionary trajectory of anatomical and reproductive features is obtained. The lack of a robust, well corroborated phylogeny of North American unionacean bivalves hinders the progress of evolutionary and ecological studies involving these species. Here we present a mitochondrial DNA (mtDNA) based phylogeny for North American unionacean mussels and compare it to previously proposed classifications. In addition, we present a 'total evidence' phylogeny which incorporates both the mtDNA sequence data and available morphological data. The molecular and total evidence phylogenies agree largely with the conclusions of a previous study based largely on immunoelectrophoretic data. North American unionaceans can be divided into two families: the Unionidae, which is comprised of most of the species and the Margaritiferidae. Within the Uniondae are two subfamilies, the Anodontinae and Ambleminae. The resultant phylogeny was used to examine the evolution of several key anatomical features including the number of gills (demibranchs) used by females to brood developing embryos, incubation length (bradytictic vs tachytictic), larval (glochidial) tooth structures, and shell texture. Both molecular and total evidence phylogenies indicate several of the aforementioned characters evolved independently or were subsequently lost or gained in several lineages.
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Affiliation(s)
- C Lydeard
- Department of Biological Sciences, University of Alabama, 35487, USA
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28
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Jemiolo DK, Pagel FT, Murgola EJ. UGA suppression by a mutant RNA of the large ribosomal subunit. Proc Natl Acad Sci U S A 1995; 92:12309-13. [PMID: 8618891 PMCID: PMC40346 DOI: 10.1073/pnas.92.26.12309] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A role for rRNA in peptide chain termination was indicated several years ago by isolation of a 168 rRNA (small subunit) mutant of Escherichia coli that suppressed UGA mutations. In this paper, we describe another interesting rRNA mutant, selected as a translational suppressor of the chain-terminating mutant trpA (UGA211) of E. coli. The finding that it suppresses UGA at two positions in trpA and does not suppress the other two termination codons, UAA and UAG, at the same codon positions (or several missense mutations, including UGG, available at one of the two positions) suggests a defect in UGA-specific termination. The suppressor mutation was mapped by plasmid fragment exchanges and in vivo suppression to domain II of the 23S rRNA gene of the rrnB operon. Sequence analysis revealed a single base change of G to A at residue 1093, an almost universally conserved base in a highly conserved region known to have specific interactions with ribosomal proteins, elongation factor G, tRNA in the A-site, and the peptidyltransferase region of 23S rRNA. Several avenues of action of the suppressor mutation are suggested, including altered interactions with release factors, ribosomal protein L11, or 16S rRNA. Regardless of the mechanism, the results indicate that a particular residue in 23S rRNA affects peptide chain termination, specifically in decoding of the UGA termination codon.
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MESH Headings
- Base Sequence
- Codon
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Genes, Bacterial
- Models, Structural
- Molecular Sequence Data
- Mutagenesis
- Nucleic Acid Conformation
- Operon
- Peptide Chain Termination, Translational
- Plasmids
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Restriction Mapping
- Ribosomal Proteins/metabolism
- Suppression, Genetic
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Affiliation(s)
- D K Jemiolo
- Department of Molecular Genetics, University of Texas M.D. Anderson Cancer Center, Houston 77030, USA
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29
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Lu M, Draper DE. On the role of rRNA tertiary structure in recognition of ribosomal protein L11 and thiostrepton. Nucleic Acids Res 1995; 23:3426-33. [PMID: 7567452 PMCID: PMC307220 DOI: 10.1093/nar/23.17.3426] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ribosomal protein L11 and an antibiotic, thiostrepton, bind to the same highly conserved region of large subunit ribosomal RNA and stabilize a set of NH4(+)-dependent tertiary interactions within the domain. In vitro selection from partially randomized pools of RNA sequences has been used to ask what aspects of RNA structure are recognized by the ligands. L11-selected RNAs showed little sequence variation over the entire 70 nucleotide randomized region, while thiostrepton required a slightly smaller 58 nucleotide domain. All the selected mutations preserved or stabilized the known secondary and tertiary structure of the RNA. L11-selected RNAs from a pool mutagenized only around a junction structure yielded a very different consensus sequence, in which the RNA tertiary structure was substantially destabilized and L11 binding was no longer dependent on NH4+. We propose that L11 can bind the RNA in two different 'modes', depending on the presence or absence of the NH4(+)-dependent tertiary structure, while thiostrepton can only recognize the RNA tertiary structure. The different RNA recognition mechanisms for the two ligands may be relevant to their different effects on protein synthesis.
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Affiliation(s)
- M Lu
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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30
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Kowalak JA, Bruenger E, McCloskey JA. Posttranscriptional modification of the central loop of domain V in Escherichia coli 23 S ribosomal RNA. J Biol Chem 1995; 270:17758-64. [PMID: 7629075 DOI: 10.1074/jbc.270.30.17758] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Knowledge of the sites, structures, and functional roles of posttranscriptional modification in rRNAs is limited, despite steadily accumulating evidence that rRNA plays a direct role in the peptidyl transferase reaction and that modified nucleotides are concentrated at the functional center of the ribosome. Using methods based on mass spectrometry, modifications have been mapped in Escherichia coli 23 S rRNA in the central loop of domain V, a region of established interaction between 23 S RNA and tRNA. Two segments of RNA were isolated following protection with oligodeoxynucleotides and nuclease digestion: residues 2423-2473 (51-mer) and 2481-2519 (39-mer). Dihydrouridine was located at position 2449, within the RNase T1 hydrolysis product 2448-ADAACAGp-2454, as evidenced by a molecular mass 2 daltons higher than the gene sequence-predicted mass. This nucleoside, which is nearly ubiquitous in tRNA (where it is involved in maintenance of loop structure), is two bases from A-2551, a previously determined site of interaction between 23 S RNA and the CCA-aminoacyl terminus of tRNA at the ribosomal P-site. The oligonucleotide 2496-CACmCUCGp-2502 was isolated and accurately mass measured, and its nucleoside constituents were characterized by high performance liquid chromatography-mass spectrometry; there was no evidence of modification at position 2501 as implied by earlier work. Using similar techniques, the modified adenosine at position 2503 was unambiguously determined to be 2-methyladenosine in the fragment 2503-m2A psi Gp-2505.
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Affiliation(s)
- J A Kowalak
- Department of Biochemistry, University of Utah, Salt Lake City 84132, USA
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31
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Abstract
Interactions between ribosomal protein L11 and a domain of large subunit rRNA have been highly conserved and are essential for efficient protein synthesis. To study the effects of L11 on rRNA folding, a homolog of the Escherichia coli L11 gene has been amplified from Bacillus stearothermophilus DNA and cloned into a phage T7 polymerase-based expression system. The expressed protein is 93% homologous to the L11 homolog from Bacillus subtilis, denatures at temperatures above 72 degrees C, and has nearly identical rRNA binding properties as the Escherichia coli L11 in terms of RNA affinity constants and their dependences on temperature, Mg2+ concentration, monovalent cation, and RNA mutations. Mg2+ and NH4+ are specifically bound by the RNA-protein complex, with apparent ion-RNA affinities of 1.6 mM-1 and 19 M-1, respectively, at 0 degree C. The effect of the thermostable L11 on the unfolding of a 60 nucleotide rRNA fragment containing its binding domain has been examined in melting experiments. The lowest temperature RNA transition, which is attributed to tertiary structure unfolding, is stabilized by approximately 25 degrees C, and the interaction has an intrinsic enthalpy of approximately 13 kcal/mol. The thermal stability of the protein-RNA complex is enhanced by increasing Mg2+ concentration and by NH4+ relative to Na+. Thus L11, NH4+, and Mg2+ all bind and stabilize the same rRNA tertiary interactions, which are conserved and presumably important for ribosome function.
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Affiliation(s)
- Y Xing
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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32
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Abstract
The stabilities and structures of a series of RNA octamers containing symmetric tandem mismatches were studied by UV melting and imino proton NMR. The free energy increments for tandem mismatch formation are found to depend upon both mismatch sequence and adjacent base pairs. The observed sequence dependence of tandem mismatch stability is UGGU > GUUG > GAAG > or = AGGA > UUUU > CAAC > or = CUUC approximately UCCU approximately CCCC approximately ACCA approximately AAAA, and the closing base pair dependence is 5'G3'C > 5'C3'G > 5'U3'A approximately 5'A3'U. These results differ from expectations based on models used in RNA folding algorithms and from the sequence dependence observed for folding of RNA hairpins. Imino proton NMR results indicate the sequence dependence is partially due to hydrogen bonding within mismatches.
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Affiliation(s)
- M Wu
- Department of Chemistry, University of Rochester, New York 14627-0216
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33
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Morton A, Tabrett A, Carder J, Barbara D. Sub-repeat sequences in the ribosomal RNA intergenic regions of Verticillium alboatrum and V. dahliae. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s0953-7562(09)80895-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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34
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Affiliation(s)
- D E Draper
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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35
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Wakefield AE, Fritscher CC, Malin AS, Gwanzura L, Hughes WT, Miller RF. Genetic diversity in human-derived Pneumocystis carinii isolates from four geographical locations shown by analysis of mitochondrial rRNA gene sequences. J Clin Microbiol 1994; 32:2959-61. [PMID: 7533779 PMCID: PMC264207 DOI: 10.1128/jcm.32.12.2959-2961.1994] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The opportunistic fungal pathogen Pneumocystis carinii is a frequent cause of pneumonia in immunocompromised hosts. In this study, we have compared the DNA sequences of a portion of the mitochondrial large-subunit rRNA gene of P. carinii (an informative locus showing up to 27% differences among isolates of P. carinii from human-, rat-, mouse-, ferret-, rabbit-, and horse-infected lungs) obtained from human-derived isolates from widely disparate geographical areas, including Britain, the United States, Brazil, and Zimbabwe. A single-base polymorphism which varied among samples was identified. Apart from this nucleotide, the DNA sequences of all samples were identical. The sequences of the British samples were shown to be stable over a period of 4 years. These data suggest that there is relatively low genetic diversity among isolates of human-derived P. carinii from different global regions.
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Affiliation(s)
- A E Wakefield
- Department of Paediatrics, John Radcliffe Hospital, Oxford, United Kingdom
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36
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Holmberg L, Melander Y, Nygård O. Probing the conformational changes in 5.8S, 18S and 28S rRNA upon association of derived subunits into complete 80S ribosomes. Nucleic Acids Res 1994; 22:2776-83. [PMID: 8052533 PMCID: PMC308247 DOI: 10.1093/nar/22.14.2776] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The participation of 18S, 5.8S and 28S ribosomal RNA in subunit association was investigated by chemical modification and primer extension. Derived 40S and 60S ribosomal subunits isolated from mouse Ehrlich ascites cells were reassociated into 80S particles. These ribosomes were treated with dimethyl sulphate and 1-cyclohexyl-3-(morpholinoethyl) carbodiimide metho-p-toluene sulfonate to allow specific modification of single strand bases in the rRNAs. The modification pattern in the 80S ribosome was compared to that of the derived ribosomal subunits. Formation of complete 80S ribosomes altered the extent of modification of a limited number of bases in the rRNAs. The majority of these nucleotides were located to phylogenetically conserved regions in the rRNA but the reactivity of some bases in eukaryote specific sequences was also changed. The nucleotides affected by subunit association were clustered in the central and 3'-minor domains of 18S rRNA as well as in domains I, II, IV and V of 5.8/28S rRNA. Most of the bases became less accessible to modification in the 80S ribosome, suggesting that these bases were involved in subunit interaction. Three regions of the rRNAs, the central domain of 18S rRNA, 5.8S rRNA and domain V in 28S rRNA, contained bases that showed increased accessibility for modification after subunit association. The increased reactivity indicates that these regions undergo structural changes upon subunit association.
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MESH Headings
- Animals
- Base Sequence
- Carcinoma, Ehrlich Tumor/metabolism
- Escherichia coli/metabolism
- Mice
- Models, Structural
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 28S/metabolism
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/metabolism
- Ribosomes/metabolism
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Affiliation(s)
- L Holmberg
- Department of Zoological Cell Biology, Arrhenius Laboratories E5, Stockholm University, Sweden
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37
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Valverde JR, Marco R, Garesse R. A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria. Proc Natl Acad Sci U S A 1994; 91:5368-71. [PMID: 7515499 PMCID: PMC43996 DOI: 10.1073/pnas.91.12.5368] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A search of sequence data bases for a tridecamer transcription termination signal, previously described in human mtDNA as being responsible for the accumulation of mitochondrial ribosomal RNAs (rRNAs) in excess over the rest of mitochondrial genes, has revealed that this termination signal occurs in equivalent positions in a wide variety of organisms from protozoa to mammals. Due to the compact organization of the mtDNA, the tridecamer motif usually appears as part of the 3' adjacent gene sequence. Because in phylogenetically widely separated organisms the mitochondrial genome has experienced many rearrangements, it is interesting that its occurrence near the 3' end of the large rRNA is independent of the adjacent gene. The tridecamer sequence has diverged in phylogenetically widely separated organisms. Nevertheless, a well-conserved heptamer--TGGCAGA, the mitochondrial rRNA termination box--can be defined. Although extending the experimental evidence of its role as a transcription termination signal in humans will be of great interest, its evolutionary conservation strongly suggests that mitochondrial rRNA transcription termination could be a widely conserved mechanism in animals. Furthermore, the conservation of a homologous tridecamer motif in one of the last 3' secondary loops of nonmitochondrial 23S-like rRNAs suggests that the role of the sequence has changed during mitochondrial evolution.
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Affiliation(s)
- J R Valverde
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid, Spain
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38
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Holmberg L, Melander Y, Nygård O. Probing the structure of mouse Ehrlich ascites cell 5.8S, 18S and 28S ribosomal RNA in situ. Nucleic Acids Res 1994; 22:1374-82. [PMID: 8190627 PMCID: PMC307993 DOI: 10.1093/nar/22.8.1374] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The secondary structure of mouse Ehrlich ascites 18S, 5.8S and 28S ribosomal RNA in situ was investigated by chemical modification using dimethyl sulphate and 1-cyclohexyl-3-(morpholinoethyl) carbodiimide metho-p-toluene sulphonate. These reagents specifically modify unpaired bases in the RNA. The reactive bases were localized by primer extension followed by gel electrophoresis. The three rRNA species were equally accessible for modification i.e. approximately 10% of the nucleotides were reactive. The experimental data support the theoretical secondary structure models proposed for 18S and 5.8/28S rRNA as almost all modified bases were located in putative single-strand regions of the rRNAs or in helical regions that could be expected to undergo dynamic breathing. However, deviations from the suggested models were found in both 18S and 28S rRNA. In 18S rRNA some putative helices in the 5'-domain were extensively modified by the single-strand specific reagents as was one of the suggested helices in domain III of 28S rRNA. Of the four eukaryote specific expansion segments present in mouse Ehrlich ascites cell 28S rRNA, segments I and III were only partly available for modification while segments II and IV showed average to high modification.
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Affiliation(s)
- L Holmberg
- Department of Zoological Cell Biology, Arrhenius Laboratories E5, Stockholm University, Sweden
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39
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Mercure S, Montplaisir S, Lemay G. Correlation between the presence of a self-splicing intron in the 25S rDNA of C.albicans and strains susceptibility to 5-fluorocytosine. Nucleic Acids Res 1993; 21:6020-7. [PMID: 7904747 PMCID: PMC310489 DOI: 10.1093/nar/21.25.6020] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Candida albicans presents a well characterized EcoRI RFLP pattern of intensely staining bands. One of these bands, the dimorphic 3.7/4.2 kbp fragment shown to originate from the ribosomal RNA-encoding regions (rDNA), has been used by several investigators to subdivide C. albicans strains in two distinct subtypes. In the present manuscript, we report that an epidemiological study of 120 C.albicans strains revealed a significant correlation between these subtypes and susceptibility to 5-fluorocytosine, an antifungal agent extensively used for biotyping C.albicans. The 4.2 kbp strains being generally more susceptible than their counterparts to this agent and one of its metabolic by-product, 5-fluorouracil. A 379 nucleotides insertion in the 25S rRNA-encoding gene of 4.2 kbp type strains was shown to be responsible for the 3.7/4.2 size difference. This intervening sequence is typical of a group I intron by its site of insertion, its predicted secondary structure, and its self-splicing capability. Assuming there is a genuine causal relationship between presence of the intron and resistance to 5-fluorocytosine, one possible mechanism suggests that inhibition of self-splicing by the insertion of 5-fluorouracil residues in the 25S rRNA precursor might be responsible for the higher susceptibility of 4.2 kbp type strains.
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Affiliation(s)
- S Mercure
- Département de Microbiologie et Immunologie, Faculté de Médecine, Université de Montréal, Québec, Canada
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40
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Blattner FR, Burland V, Plunkett G, Sofia HJ, Daniels DL. Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res 1993; 21:5408-17. [PMID: 8265357 PMCID: PMC310579 DOI: 10.1093/nar/21.23.5408] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We present the sequence of 176 kilobases of the Escherichia coli K-12 genome, from katG at 89.2 to an open reading frame (ORF) of unknown function at 92.8 minutes on the genetic map. This brings the total of contiguous sequence from the E. coli genome project to 500 kb (81.5 to 92.8 minutes). This segment contains 134 putative coding genes (ORFs) of which 66 genes were previously identified. Eight new genes--acs, pepE, and nrfB-G--were identified as well as the previously mapped gldA and alr genes. Still, 58 ORFs remain unidentified despite literature and similarity searches. The arrangement of proposed genes relative to possible promoters and terminators suggests 55 potential transcription units. Other features include 13 REP elements, one IRU (ERIC) repeat, 59 computer-predicted bends, 42 Chi sites and one new grey hole. Sixteen signal peptides were found, including those of lamB, btuB, and malE. Two ribosomal RNA loci, rrnB and rrnE, are located in this segment, so we have now sequenced four of the seven E. coli rRNA loci. Comparison of the rRNA loci reveals some differences in the ribosomal structural RNAs which are generally compatible with the proposed secondary structures.
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Affiliation(s)
- F R Blattner
- Laboratory of Genetics, University of Wisconsin, Madison 53706
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41
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Wang YX, Lu M, Draper DE. Specific ammonium ion requirement for functional ribosomal RNA tertiary structure. Biochemistry 1993; 32:12279-82. [PMID: 8241113 DOI: 10.1021/bi00097a002] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In compactly folded RNAs, coordination or hydrogen bonding of cations in specific sites is a potentially important aspect of the tertiary structure. NH4+ specifically stabilizes the tertiary structure of a conserved, 58-nt fragment of the large subunit ribosomal RNA, as judged in two ways: a melting transition associated with tertiary interactions is sharpened and stabilized more effectively by NH4+ than by any alkali metal cation, and the affinity of the RNA fragment for ribosomal protein L11 or the antibiotic thiostrepton is approximately 10-fold stronger when measured in NH4+ than in Na+. The dependence of the melting temperature on NH4+ concentration shows that a single bound ion is responsible for these effects. The requirement of different ribosome functions for NH4+ suggests that other such sites exist in ribosomal RNAs.
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Affiliation(s)
- Y X Wang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
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42
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Structure of 16S and 23S Ribosomal RNA Genes in Campylobacter Species: Phylogenetic Analysis of the Genus Campylobacter and Presence of Internal Transcribed Spacers. Syst Appl Microbiol 1993. [DOI: 10.1016/s0723-2020(11)80266-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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Mercure S, Rougeau N, Montplaisir S, Lemay G. Complete nucleotide sequence of Candida albicans 5.8S rRNA coding gene and flanking internal transcribed spacers. Nucleic Acids Res 1993; 21:4640. [PMID: 8233804 PMCID: PMC311204 DOI: 10.1093/nar/21.19.4640] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- S Mercure
- Departement de Microbiologie et Immunologie, Université de Montréal, Québec, Canada
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44
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Van Camp G, Chapelle S, De Wachter R. Amplification and sequencing of variable regions in bacterial 23S ribosomal RNA genes with conserved primer sequences. Curr Microbiol 1993; 27:147-51. [PMID: 7691306 DOI: 10.1007/bf01576012] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Published bacterial 23S ribosomal RNA sequences were aligned, and universally conserved regions flanking highly variable regions were looked for. In strategically positioned conserved regions, six oligonucleotides suitable for polymerase chain reaction (PCR) and sequencing were designed, allowing fast sequencing of four of the most variable 23S rRNA regions. Two other primers were designed for PCR amplification of nearly complete 23S rRNA genes. All these primers successfully amplified fragments of 23S rRNA genes from seven unrelated bacteria. Four primers were used to determine 938 bp of sequence for Campylobacter jejuni subsp. jejuni. These results indicate that the oligonucleotide sequences presented here are useful for PCR amplification and sequence determination of variable 23S rRNA regions for a broad variety of eubacterial species.
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Affiliation(s)
- G Van Camp
- Department of Biochemistry, University of Antwerp (UIA), Belgium
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45
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Johnston DA, Kane RA, Rollinson D. Small subunit (18S) ribosomal RNA gene divergence in the genus Schistosoma. Parasitology 1993; 107 ( Pt 2):147-56. [PMID: 8414669 DOI: 10.1017/s0031182000067251] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
An entire 18S rRNA gene sequence from Schistosoma spindale (1990 bases) and partial 18S rRNA gene sequences from S. haematobium (1950 bases) and S. japonicum (1648 bases) have been determined. Together with the previously published sequence of the S. mansoni 18S rRNA gene, these data encompass the 4 recognized Schistosoma species groups. Although Schistosoma 18S rRNA genes are highly conserved, the sequences permit a preliminary molecular phylogeny to be established for the genus. This identifies S. haematobium and S. spindale as sister taxa in a clade with S. mansoni. S. japonicum does not appear to be closely related to this clade. Much of the observed variation occurs within a 'hypervariable' stretch of the gene corresponding to part of the V4 region of 18S rRNA. Despite this variation, the 3 new sequences fit models of 18S rRNA secondary structure predicted from the S. mansoni sequence.
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Affiliation(s)
- D A Johnston
- Department of Zoology, The Natural History Museum, London
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46
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Van de Peer Y, Neefs JM, De Rijk P, De Wachter R. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock. J Mol Evol 1993; 37:221-32. [PMID: 8411212 DOI: 10.1007/bf02407359] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The detailed descriptions now available for the secondary structure of small-ribosomal-subunit RNA, including areas of highly variable primary structure, facilitate the alignment of nucleotide sequences. However, for optimal exploitation of the information contained in the alignment, a method must be available that takes into account the local sequence variability in the computation of evolutionary distance. A quantitative definition for the variability of an alignment position is proposed in this study. It is a parameter in an equation which expresses the probability that the alignment position contains a different nucleotide in two sequences, as a function of the distance separating these sequences, i.e., the number of substitutions per nucleotide that occurred during their divergence. This parameter can be estimated from the distance matrix resulting from the conversion of pairwise sequence dissimilarities into pairwise distances. Alignment positions can then be subdivided into a number of sets of matching variability, and the average variability of each set can be derived. Next, the conversion of dissimilarity into distance can be recalculated for each set of alignment positions separately, using a modified version of the equation that corrects for multiple substitutions and changing for each set the parameter that reflects its average variability. The distances computed for each set are finally averaged, giving a more precise distance estimation. Trees constructed by the algorithm based on variability calibration have a topology markedly different from that of trees constructed from the same alignments in the absence of calibration. This is illustrated by means of trees constructed from small-ribosomal-subunit RNA sequences of Metazoa. A reconstruction of vertebrate evolution based on calibrated alignments matches the consensus view of paleontologists, contrary to trees based on uncalibrated alignments. In trees derived from sequences covering several metazoan phyla, artefacts in topology that are probably due to a high clock rate in certain lineages are avoided.
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Affiliation(s)
- Y Van de Peer
- Department Biochemie, Universiteit Antwerpen (UIA), Belgium
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47
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Lapeyre B, Michot B, Feliu J, Bachellerie JP. Nucleotide sequence of the Schizosaccharomyces pombe 25S ribosomal RNA and its phylogenetic implications. Nucleic Acids Res 1993; 21:3322. [PMID: 8341608 PMCID: PMC309776 DOI: 10.1093/nar/21.14.3322] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- B Lapeyre
- Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France
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48
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Gutell RR, Gray MW, Schnare MN. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. Nucleic Acids Res 1993; 21:3055-74. [PMID: 8332527 PMCID: PMC309733 DOI: 10.1093/nar/21.13.3055] [Citation(s) in RCA: 297] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- R R Gutell
- Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347
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49
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Mercure S, Rougeau N, Montplaisir S, Lemay G. The nucleotide sequence of the 25S rRNA-encoding gene from Candida albicans. Nucleic Acids Res 1993; 21:1490. [PMID: 8464743 PMCID: PMC309338 DOI: 10.1093/nar/21.6.1490] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- S Mercure
- Département de Microbiologie et Immunologie, Université de Montréal, Québec, Canada
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50
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Ludwig W, Kirchhof G, Klugbauer N, Weizenegger M, Betzl D, Ehrmann M, Hertel C, Jilg S, Tatzel R, Zitzelsberger H, Liebl S, Hochberger M, Shah J, Lane D, Wallnöfer PR, Scheifer KH. Complete 23S Ribosomal RNA Sequences of Gram-positive Bacteria with a Low DNA G+C Content. Syst Appl Microbiol 1992. [DOI: 10.1016/s0723-2020(11)80107-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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