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Appels R, Wang P, Islam S. Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:686586. [PMID: 35003148 PMCID: PMC8739226 DOI: 10.3389/fpls.2021.686586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
We review the coordinated production and integration of the RNA (ribosomal RNA, rRNA) and protein (ribosomal protein, RP) components of wheat cytoplasmic ribosomes in response to changes in genetic constitution, biotic and abiotic stresses. The components examined are highly conserved and identified with reference to model systems such as human, Arabidopsis, and rice, but have sufficient levels of differences in their DNA and amino acid sequences to form fingerprints or gene haplotypes that provide new markers to associate with phenotype variation. Specifically, it is argued that populations of ribosomes within a cell can comprise distinct complements of rRNA and RPs to form units with unique functionalities. The unique functionalities of ribosome populations within a cell can become central in situations of stress where they may preferentially translate mRNAs coding for proteins better suited to contributing to survival of the cell. In model systems where this concept has been developed, the engagement of initiation factors and elongation factors to account for variation in the translation machinery of the cell in response to stresses provided the precedents. The polyploid nature of wheat adds extra variation at each step of the synthesis and assembly of the rRNAs and RPs which can, as a result, potentially enhance its response to changing environments and disease threats.
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Affiliation(s)
- Rudi Appels
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
- Faculty of Veterinary and Agricultural Science, Melbourne, VIC, Australia
| | - Penghao Wang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Shahidul Islam
- Centre for Crop Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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2
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Learn GH, Schaal BA. POPULATION SUBDIVISION FOR RIBOSOMAL DNA REPEAT VARIANTS IN
CLEMATIS FREMONTII. Evolution 2017; 41:433-438. [DOI: 10.1111/j.1558-5646.1987.tb05809.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/1986] [Accepted: 11/11/1986] [Indexed: 11/30/2022]
Affiliation(s)
- Gerald H. Learn
- Department of Biology Washington University St. Louis MO 63130
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3
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Affiliation(s)
- R. A. McIntosh
- University of Sydney; Plant Breeding Institute; Castle Hill, N.S.W. Australia
| | - Jane E. Cusick
- University of Sydney; Plant Breeding Institute; Castle Hill, N.S.W. Australia
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4
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Decatur WA, Schnare MN. Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol 2008; 28:3089-100. [PMID: 18332121 PMCID: PMC2423156 DOI: 10.1128/mcb.01574-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 10/23/2007] [Accepted: 02/26/2008] [Indexed: 12/29/2022] Open
Abstract
The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (Psis) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of Psi formation in 5S and 5.8S rRNA in which the unassigned Psis occur. We show that while the formation of the Psi in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the Psi in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the Psi in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis.
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MESH Headings
- Ascomycota/genetics
- Ascomycota/metabolism
- Base Sequence
- DNA Primers/genetics
- Gene Deletion
- Genes, Fungal
- Genetic Complementation Test
- Hydro-Lyases/genetics
- Hydro-Lyases/metabolism
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Pseudouridine/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5.8S/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Homology, Nucleic Acid
- Spliceosomes/metabolism
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Affiliation(s)
- Wayne A Decatur
- Department of Biochemistry and Molecular Biology, 903 Lederle Graduate Research Tower, University of Massachusetts, Amherst, MA 01003, USA.
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5
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Barciszewska MZ, Mashkova TD, Kisselev L, Barciszewski J. The primary structure of maize and tobacco 5 S rRNA. FEBS Lett 2001. [DOI: 10.1016/0014-5793(85)80127-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Lane BG. Sequences in the 3'-terminal coding regions of 5 S and 18 S rRNA genes may contribute to co-ordinated expression of 5 S rRNA and pre(18 S/5.8 S/26 S) rRNA genes. FEBS Lett 2001. [DOI: 10.1016/0014-5793(85)81328-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Vandenberghe A, Chen MW, Dams E, de Baere R, de Roeck E, Huysmans E, de Wachter R. The corrected nucleotide sequences of 5 S RNAs from six angiosperms. FEBS Lett 2001. [DOI: 10.1016/0014-5793(84)80452-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Schnare MN, Collings JC, Spencer DF, Gray MW. The 28S-18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor. Nucleic Acids Res 2000; 28:3452-61. [PMID: 10982863 PMCID: PMC110749 DOI: 10.1093/nar/28.18.3452] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2000] [Revised: 07/17/2000] [Accepted: 07/28/2000] [Indexed: 11/12/2022] Open
Abstract
In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from approximately 11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an approximately 55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A' pre-rRNA processing sites within the 5' external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5' ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C. fasciculata and Trypanosoma brucei involves 3'-terminal addition of three A residues that are not present in the corresponding DNA sequences.
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MESH Headings
- Animals
- Base Pairing
- Base Sequence
- Conserved Sequence
- Crithidia fasciculata/genetics
- Crithidia fasciculata/metabolism
- DNA, Protozoan/genetics
- DNA, Protozoan/metabolism
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Genetic Heterogeneity
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Repetitive Sequences, Nucleic Acid
- Restriction Mapping
- Sequence Alignment
- Sequence Analysis, DNA
- Trypanosoma brucei brucei/genetics
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Affiliation(s)
- M N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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9
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Schnare MN, Gray MW. Structural conservation and variation among U5 small nuclear RNAs from trypanosomatid protozoa. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1490:362-6. [PMID: 10684982 DOI: 10.1016/s0167-4781(00)00009-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
U5 snRNAs in trypanosomatid protozoa do not contain the trimethylguanosine cap structures that are often targeted in snRNA isolation procedures. As a result, the trypanosomatids are not well represented in the database of available U5 snRNA sequences. We have isolated and determined the sequence of the U5 snRNA from Crithidia fasciculata. Comparison with previously published trypanosomatid U5 snRNA sequences allows us to deduce the pattern of structural conservation and variation among these very divergent snRNA molecules.
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Affiliation(s)
- M N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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10
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Abstract
In trypanosomatid protozoa, all mRNAs obtain identical 5'-ends by trans-splicing of the 5'-terminal 39 nucleotides of a small spliced leader RNA to appropriate acceptor sites in pre-mRNA. Although this process involves spliceosomal small nuclear (sn) RNAs, it is thought that trypanosomatids do not contain a homolog of the cis-spliceosomal U1 snRNA. We show here that a trypanosomatid protozoon, Crithidia fasciculata, contains a novel small RNA that displays several features characteristic of a U1 snRNA, including (i) a methylguanosine cap and additional 5'-terminal modifications, (ii) a potential binding site for common core proteins that are present in other trans-spliceosomal ribonucleoproteins, (iii) a U1-like 5'-terminal sequence, and (iv) a U1-like stem/loop I structure. Because trypanosomatid pre-mRNAs do not appear to contain cis-spliced introns, we argue that this previously unrecognized RNA species is a good candidate to be a trans-spliceosomal U1 snRNA.
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Affiliation(s)
- M N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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11
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Suh Y, Thien LB, Zimmer EA. Nucleotide sequences of the internal transcribed spacers and 5.8S rRNA gene in Canella winterana (Magnoliales; Canellaceae). Nucleic Acids Res 1992; 20:6101-2. [PMID: 1461743 PMCID: PMC334481 DOI: 10.1093/nar/20.22.6101] [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: 12/27/2022] Open
Affiliation(s)
- Y Suh
- Laboratory of Molecular Systematics, Smithsonian Institution, Washington, DC 20560
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12
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Abstract
We have isolated cytoplasmic ribosomes from Euglena gracilis and characterized the RNA components of these particles. We show here that instead of the four rRNAs (17-19 S, 25-28 S, 5.8 S and 5 S) found in typical eukaryotic ribosomes, Euglena cytoplasmic ribosomes contain 16 RNA components. Three of these Euglena rRNAs are the structural equivalents of the 17-19 S, 5.8 S and 5 S rRNAs of other eukaryotes. However, the equivalent of 25-28 S rRNA is found in Euglena as 13 separate RNA species. We demonstrate that together with 5 S and 5.8 S rRNA, these 13 RNAs are all components of the large ribosomal subunit, while a 19 S RNA is the sole RNA component of the small ribosomal subunit. Two of the 13 pieces of 25-28 S rRNA are not tightly bound to the large ribosomal subunit and are released at low (0 to 0.1 mM) magnesium ion concentrations. We present here the complete primary sequences of each of the 14 RNA components (including 5.8 S rRNA) of Euglena large subunit rRNA. Sequence comparisons and secondary structure modeling indicate that these 14 RNAs exist as a non-covalent network that together must perform the functions attributed to the covalently continuous, high molecular weight, large subunit rRNA from other systems.
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Affiliation(s)
- M N Schnare
- Department of Biochemistry, Dalhousie University Halifax, Nova Scotia, Canada
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13
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Hanic-Joyce P, Gray M. Processing of transfer RNA precursors in a wheat mitochondrial extract. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)77417-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Barciszewska MZ, Mashkova TD, Barciszewski J. The primary structure of lupin seed 5.8 S ribosomal RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1049:343-5. [PMID: 2383589 DOI: 10.1016/0167-4781(90)90108-e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The lack of colinearity between nucleotide sequence of the lupin 5.8 S rDNA gene (Rafalski, A.J., Wiewiórowski, M. and Soll, D. (1983) FEBS Lett. 152, 241-246) and 5.8 S rRNA of other plants (Erdmann, V.A. and Wolters, J. (1986) Nucleic Acids Res. 14, r1-r59.) prompted us to clarify this point by sequencing the native lupin 5.8 S rRNA. The sequence analysis was carried out using enzymatic and chemical methods. Lupin seed 5.8 S rRNA contains 164 nucleotides, including four modified ones: two residues of 2'-O-methylguanosine, one pseudouridine and one 2'-O-methyladenosine. The nucleotide sequence homology with the other plant 5.8 S rRNAs is approx. 88-96%.
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Affiliation(s)
- M Z Barciszewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań
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15
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Melekhovets YuF, Troitsky AV. Comparative analysis of 5.8 S rRNA from Ephedra kokanica Regl. (Gymnospermae) and other plant species. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1048:294-6. [PMID: 2322582 DOI: 10.1016/0167-4781(90)90070-i] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
5.8 S rRNA from the gymnosperm Ephedra kokanica Regl. (EMBL Data Library accession No. X15676) has been sequenced. It is 161 nucleotides long and contains three 2'-O-methylated residues--two adenosines and one guanosine. No pseudouridine have been detected. E. kokanica 5.8 S rRNA, as those from other plant species, can form a secondary structure with paired 5'- and 3'-terminal regions. 5.8 S rRNAs of seed plants differ from the moss Mnium reguicum 5.8 S rRNA in that they have longer variable 'GC-rich' hairpins with insertions in the loop region. 5.8 S rRNA of E. kokanica reveals 69 and 82% of homology with that of moss and five angiosperm species, respectively. The posttranscriptional modification pattern of plant 5.8 S rRNAs is not strictly conservative.
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Affiliation(s)
- Melekhovets YuF
- A.N. Belozersky Laboratory of Molecular Biology and Bioorganic Chemistry, Moscow State University, U.S.S.R
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16
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Torres RA, Ganal M, Hemleben V. GC balance in the internal transcribed spacers ITS 1 and ITS 2 of nuclear ribosomal RNA genes. J Mol Evol 1990; 30:170-81. [PMID: 2107331 DOI: 10.1007/bf02099943] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The internal transcribed spacer (ITS) 1 and 2, the 5.8S rRNA gene, and adjacent 18S rRNA and 25S rRNA coding regions of two Cucurbitaceae (Cucurbita pepo, zucchini, ITS 1: 187 bp, and ITS 2: 252 bp in length, and Cucumis sativus, cucumber, ITS 1: 229 bp, and ITS 2: 245 bp in length) have been sequenced. The evolutionary pattern shown by the ITSs of these plants is different from that found in vertebrates. Deletions, insertions, and base substitutions have occurred in both spacers; however, it is obvious that some selection pressure is responsible for the preservation of stem-loop structures. The dissimilarity of the 5' region of ITS 2 found in higher plants has consequences for proposed models on U3 snRNA-ITS 2 interaction in higher eukaryotes. The two investigated Cucurbitaceae species show a G + C content of ITS 1 that nearly equals that of ITS 2. An analysis of the ITS sequences reveals that in 19 out of 20 organisms published, the G + C content of ITS 1 nearly equals that of ITS 2, although it ranges from 20% to 90% in different organisms (GC balance). Moreover, the balanced G + C content of the ITSs in a given species seems to be similar to that of so-called expansion segments (ESs) in the 25/28S rRNA coding region. Thus, ITSs show a phenomenon called molecular coevolution with respect to each other and to the ESs. In the ITSs of Cucurbitaceae the balanced G + C composition is at least partly achieved by C to T transitions, via deamination of 5-methylcytosine. Other mutational events must be taken into account. The appearance of this phenomenon is discussed in terms of functional constraints linked to the structures of these spacers.
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Affiliation(s)
- R A Torres
- Lehrstuhl für Allgemeine Genetik, Universität Tübingen, Federal Republic of Germany
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17
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Yokota Y, Kawata T, Iida Y, Kato A, Tanifuji S. Nucleotide sequences of the 5.8S rRNA gene and internal transcribed spacer regions in carrot and broad bean ribosomal DNA. J Mol Evol 1989; 29:294-301. [PMID: 2514271 DOI: 10.1007/bf02103617] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleotide sequences of the first and second internal transcribed spacers (ITS1 and ITS2, respectively) of ribosomal DNA (rDNA) from two dicot plants, carrot and broad bean, were determined. These sequences were compared with those of rice, a monocot plant, and other eukaryotic organisms. Both types of ITS region in some species of Angiospermae were the shortest among all eukaryotes so far examined and showed a wide range of variation in their G+C content, in contrast to a general trend toward very high G+C content in animals. Phylogenetic relationships of plants with animals and lower eukaryotes were considered using the nucleotide sequences of carrot and broad bean 5.8S rDNA that were determined in the present study, together with that of wheat 5.8S rRNA, which has been reported previously.
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Affiliation(s)
- Y Yokota
- Department of Botany, Faculty of Science, Hokkaido University, Sapporo, Japan
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18
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Unusual pattern of ribonucleic acid components in the ribosome of Crithidia fasciculata, a trypanosomatid protozoan. Mol Cell Biol 1988. [PMID: 6965102 DOI: 10.1128/mcb.1.4.347] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous study from this laboratory, presumptive ribosomal ribonucleic acid (RNA) species were identified in the total cellular RNA directly extracted from intact cells of the trypanosomatid protozoan Crithidia fasciculata (M. W. Gray, Can. J. Biochem. 57:914-926, 1979). The results suggested that the C. fasciculata ribosome might be unusual in containing three novel, low-molecular-weight ribosomal RNA components, designated e, f, and g (apparent chain lengths 240, 195, and 135 nucleotides, respectively), in addition to analogs of eucaryotic 5S (species h) and 5.8S (species i) ribosomal RNAs. In the present study, all of the presumptive ribosomal RNAs were indeed found to be associated with purified C. fasciculata ribosomes, and their localization was investigated in subunits produced under different conditions of ribosome dissociation. When ribosomes were dissociated in a high-potassium (880 mM K+, 12.5 mM Mg2+) medium, species e to i were all found in the large ribosomal subunit, which also contained an additional, transfer RNA-sized component (species j). However, when subunits were prepared in a low-magnesium (60 mM K+, 0.1 mM Mg2+) medium, two of the novel species (e and g) did not remain with the large subunit, but were released, apparently as free RNAs. Control experiments have eliminated the possibility that the small RNAs are generated by quantitative and highly specific (albeit artifactual) ribonuclease cleavage of large ribosomal RNAs during isolation. In terms of RNA composition and dissociation properties, therefore, the ribosome of C. fasciculata is the most "atypical" eucaryotic ribosome yet described. These observations raise interesting questions about the function and evolutionary origin of C. fasciculata ribosomes and about the organization and expression of ribosomal RNA genes in this organism.
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19
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Barciszewski J, Bratek-Wiewiórowska MD, Górnicki P, Naskret-Barciszewska M, Wiewiórowski M, Zielenkiewicz A, Zielenkiewicz W. Comparative calorimetric studies on the dynamic conformation of plant 5S rRNA. I. Thermal unfolding pattern of lupin seeds and wheat germ 5S rRNAs, also in the presence of magnesium and sperminium cations. Nucleic Acids Res 1988; 16:685-701. [PMID: 3340550 PMCID: PMC334685 DOI: 10.1093/nar/16.2.685] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
An attempt has been made to correlate differential scanning calorimetry melting profiles of 5S rRNAs from lupin seeds (L.s.) and wheat germ (W.g.) with their structure. It is suggested that the observed differences in thermal unfolding are due to differences in RNA nucleotide sequence and as a consequence in higher order structures. Interesting effects induced by magnesium cation, perprotonated and permethylated sperminium tetracations are discussed. It is suggested that the difference in the stabilizing effect of the three cations results from different mode of their interactions with RNA. "Pure" electrostatic interactions expected for permethylated tetracations are rather weak due to the steric hindrance around each positively charged nitrogen atom. Electrostatic interactions of the other two cations are significantly enhanced by coordination bonding for magnesium and by hydrogen bonding for protonated sperminium cation.
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Affiliation(s)
- J Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan
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20
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Spencer DF, Collings JC, Schnare MN, Gray MW. Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata. EMBO J 1987; 6:1063-71. [PMID: 16453755 PMCID: PMC553503 DOI: 10.1002/j.1460-2075.1987.tb04859.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In Crithidia fasciculata, a trypanosomatid protozoan, the nuclear-encoded ;28S' rRNA is multiply fragmented, comprising two large (c and d) and four small (e, f, g and j) RNA species. We have determined that the coding sequences for these RNAs (and that of the 5.8S rRNA, species i) are separated from one another by spacer sequences ranging in size from 31 to 416 bp. Coding and spacer sequences are presumably co-transcribed, with excision of the latter during post-transcriptional processing generating a highly fragmented large subunit (LSU) rRNA. Secondary structure modelling indicates that the C. fasciculata LSU rRNA complex (seven segments, including 5.8S rRNA) is held together in part by long-range intermolecular base pairing interactions that are characteristic of intramolecular interactions in the covalently continuous LSU (23S) rRNA of Escherichia coli. At least one functionally critical region (encompassing the alpha-sarcin cleavage site) is contained in a small RNA species (f) rather than in one of the two large RNAs. Within a proposed secondary structure model of C. fasciculata LSU rRNA, discontinuities between the different segments (created by spacer excision) map to regions that are highly variable in structure in covalently continuous LSU rRNAs. We suggest that ;rRNA genes in pieces' and discontinuous rRNAs may represent an evolutionarily ancient pattern.
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Affiliation(s)
- D F Spencer
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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21
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Li SJ, Wu JJ, Marshall AG. 500-MHz proton homonuclear Overhauser evidence for additional base pair in the common arm of eukaryotic ribosomal 5S RNA: wheat germ. Biochemistry 1987; 26:1578-85. [PMID: 3109468 DOI: 10.1021/bi00380a014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A "common-arm" fragment from wheat germ (Triticum aestivum) 5S RNA has been produced by enzymatic cleavage with RNase T1 and sequenced via autoradiography of electrophoresis gels for the end-labeled fragments obtained by further RNase T1 partial digestion. The existence, base pair composition, and base pair sequence of the common arm are demonstrated for the first time by means of proton 500-MHz nuclear magnetic resonance. From Mg2+ titration, temperature variation, ring current calculations, sequence comparisons, and proton homonuclear Overhauser enhancement experiments, additional base pairs in the common arm of the eukaryotic 5S RNA secondary structure are detected. Two base pairs, G41 X C34 and A42 X U33 in the hairpin loop, could account for the lack of binding between the conserved GAAC segment of 5S RNA and the conserved Watson-Crick-complementary GT psi C segment of tRNAs.
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22
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23
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Andersen J, Delihas N. Characterization of RNA-protein interactions in 7 S ribonucleoprotein particles from Xenopus laevis oocytes. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)35873-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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24
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Schnare MN, Collings JC, Gray MW. Structure and evolution of the small subunit ribosomal RNA gene of Crithidia fasciculata. Curr Genet 1986; 10:405-10. [PMID: 2832072 DOI: 10.1007/bf00418414] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We present the cloning and sequence analysis of the nuclear-encoded Crithidia fasciculata small subunit (SSU) rRNA gene, the longest (2,206 bp) such gene yet characterized by direct sequence analysis. Much of the sequence can be folded to fit a phylogenetically conserved secondary structure model, with the additional length of this gene being accommodated within discrete variable domains that are present in eukaryotic SSU rRNAs. On the basis of sequence comparisons, we conclude that Crithidia contains the most highly diverged SSU rRNA described to date among the eukaryotes, and therefore represents one of the earliest branchings within the eukaryotic primary kingdom.
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Affiliation(s)
- M N Schnare
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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25
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Takaiwa F, Oono K, Sugiura M. Nucleotide sequence of the 17S-25S spacer region from rice rDNA. PLANT MOLECULAR BIOLOGY 1985; 4:355-364. [PMID: 24310938 DOI: 10.1007/bf02418257] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The nucleotide sequence of a spacer region between rice 17S and 25S rRNA genes (rDNAs) has been determined. The coding regions for the mature 17S, 5.8S and 25S rRNAs were identified by sequencing terminal regions of these rRNAs. The first internal transcribed spacer (ITS1), between 17S and 5.8S rDNAs, is 194-195 bp long. The second internal transcribed spacer (ITS2), between 5.8S and 25S rDNAs, is 233 bp long. Both spacers are very rich in G+C, 72.7% for ITS1 and 77.3% for ITS2. The 5.8S rDNA is 163-164 bp long and similar in primary and secondary structures to other eukaryotic 5.8S rDNAs. The 5.8S rDNA is capable of interacting with the 5' terminal region of 25S rDNA.
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Affiliation(s)
- F Takaiwa
- National Institute of Agrobiological Resources, Tsukuba Science City, 305, Yatabe Ibaraki, Japan
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26
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Behlke J, Misselwitz R, Welfle H. Hydrodynamic properties of 5.8S rRNA, salt and temperature effects. Int J Biol Macromol 1985. [DOI: 10.1016/0141-8130(85)90026-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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28
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Schnare MN, Heinonen TY, Young PG, Gray MW. Phenylalanine and tyrosine transfer RNAs encoded by Tetrahymena pyriformis mitochondrial DNA: primary sequence, post-transcriptional modifications, and gene localization. Curr Genet 1985; 9:389-93. [PMID: 3939713 DOI: 10.1007/bf00421610] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have isolated Phe and Tyr tRNAs from Tetrahymena pyriformis mitochondria and have determined that these are "native" species, encoded by the mtDNA. A single gene for the tRNA(Phe) has been positioned 12-14 kbp from the left end of the linear Tetrahymena mtDNA, while duplicate tRNA(Tyr) genes have been localized within the inverted terminal repeats of this genome. Primary sequence analysis demonstrates that the tRNA(Tyr) has all of the characteristic primary and secondary structural features of a normal tRNA; however, the tRNA(Phe) displays several atypical features, including (i) replacement of the usual T psi sequence by UC, (ii) a U.U pair in the T psi C stem, and (iii) an extra 5'-nucleotide (U).
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Affiliation(s)
- M N Schnare
- Dept. of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Great Britain
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29
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Müller JJ, Misselwitz R, Zirwer D, Damaschun G, Welfle H. A-form to A'-form conformational switch of double helices in rat liver 5S and 5.8S rRNA. Solution X-ray scattering evidence and circular dichroic measurements. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 148:89-95. [PMID: 3979398 DOI: 10.1111/j.1432-1033.1985.tb08811.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The wide-angle X-ray scattering of rat liver 5S rRNA and 5.8S rRNA molecules showed significant differences in the positions of the scattering maxima when dissolved in Mg2+-containing Tris/HCl buffer or in Mg2+-depleted buffer. A comparison of the experimental curves with theoretical curves calculated from atomic coordinates of double-helical models proved a switch from A form to A' form of the double-helical regions within the molecules by changing the buffer conditions. This result was supported by circular dichroic measurements. The A to A' transition may have important consequences for RNA-protein interactions.
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30
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Skuzeski JM, Jendrisak JJ. A family of wheat embryo U2 snRNAs. PLANT MOLECULAR BIOLOGY 1985; 4:181-193. [PMID: 24310755 DOI: 10.1007/bf02418765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/1984] [Revised: 08/27/1984] [Accepted: 09/10/1984] [Indexed: 06/02/2023]
Abstract
Evidence is presented for the existence of small nuclear RNAs in a higher plant species. Based on subcellular fractionation experiments, wheat embryos contain at least four putative snRNAs, one of which co-migrates on SDS-polyacrylamide gels with a relatively abundant cytoplasmic RNA, W1. We purified W1 from ribosome-free high speed supernatant fractions for characterization studies. Electrophoresis under partially denaturing conditions resolves this RNA into several components which bear m3 (2, 2, 7) G-5' caps and strongly resemble vertebrate U2 snRNA on the basis of modified nucleotide content. Preliminary sequence analyses indicate that wheat embryos contain at least three U2-like RNAs which possess slightly different sequences near their 3' ends.
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Affiliation(s)
- J M Skuzeski
- Department of Botany, University of Minnesota, 55108, St. Paul, MN, U.S.A
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31
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Erdmann VA, Wolters J, Huysmans E, De Wachter R. Collection of published 5S, 5.8S and 4.5S ribosomal RNA sequences. Nucleic Acids Res 1985; 13 Suppl:r105-53. [PMID: 3923444 PMCID: PMC320506 DOI: 10.1093/nar/13.suppl.r105] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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32
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33
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Chromatin organization and methylation patterns of wheat 5 S RNA genes (Triticum aestivum var. hardi). ACTA ACUST UNITED AC 1984. [DOI: 10.1016/0304-4211(84)90215-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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34
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35
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Hanas JS, Bogenhagen DF, Wu CW. Binding of Xenopus transcription factor A to 5S RNA and to single stranded DNA. Nucleic Acids Res 1984; 12:2745-58. [PMID: 6369252 PMCID: PMC318703 DOI: 10.1093/nar/12.6.2745] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Footprint competition assays are utilized to study the binding of Xenopus transcription factor A to a variety of single-stranded nucleic acids. The addition of Xenopus oocyte, yeast, or wheat germ 5S RNA as footprint competitors reveals that factor A binds these 5S RNAs with similar affinity. In contrast, factor A does not bind to E.coli 5S RNA or wheat germ tRNA in this assay. Factor A binding to single stranded DNA is also examined using footprint competition. Factor A binds preferentially to non-specific single stranded (M13) DNA versus double stranded (pBR322) DNA. Factor A binds equally well to single stranded DNA fragments containing either the coding or non-coding strands of the 5S RNA gene. Using single stranded M13 DNA as a competitor, the factor A-5S RNA gene complex is found to dissociate with a half-life of 5-6 min.
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36
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Tissue Culture and Genetic Engineering in Rice. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/b978-0-444-99615-2.50019-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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37
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Erdmann VA, Wolters J, Huysmans E, Vandenberghe A, De Wachter R. Collection of published 5S and 5.8S ribosomal RNA sequences. Nucleic Acids Res 1984; 12 Suppl:r133-66. [PMID: 6728686 PMCID: PMC320007 DOI: 10.1093/nar/12.suppl.r133] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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38
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Nazar RN, Wildeman AG. Three helical domains form a protein binding site in the 5S RNA-protein complex from eukaryotic ribosomes. Nucleic Acids Res 1983; 11:3155-68. [PMID: 6344007 PMCID: PMC325955 DOI: 10.1093/nar/11.10.3155] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A ribosomal protein binding site in the eukaryotic 5S rRNA has been delineated by examining the effect of sequence variation and nucleotide modification on the RNA's ability to exchange into the EDTA-released, yeast ribosomal 5S RNA-protein complex. 5S RNAs of divergent sequence from a variety of eukaryotic origins could be readily exchanged into the yeast complex but RNA from bacterial origins was rejected. Nucleotide modifications in any of three analogous helical regions in eukaryotic 5S RNAs of differing origin reduced the ability of this RNA molecule to form homologous or heterologous RNA-protein complexes. Because sequence comparisons did not indicate common nucleotide sequences in the interacting helical regions, a model is suggested in which the eukaryotic 5S RNA binding protein does not simply recognize specific nucleotide sequences but interacts with three strategically oriented helical domains or functional groups within these domains. Two of the domains bear a limited sequence homology with each other and contain an unpaired nucleotide or "bulge" similar to that recently reported for one of the 5S RNA binding proteins in Escherichia coli (Peattie, D.A., Douthwaite, S., Garrett, R.A. and Noller, H.F. (1981) Proc. Natl. Acad. Sci. 78, 7331-7335). The results further indicate that the single ribosomal protein of eukaryotic 5S RNA-protein complexes interacts with the same region of the 5S rRNA molecule as do the multiple protein components in complexes of prokaryotic origin.
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39
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Abstract
The sequences of 5S ribosomal RNAs from a wide-range of organisms have been compared. All sequences fit a generalized 5S RNA secondary structural model. Twenty-three nucleotide positions are found universally, i.e., in 5S RNAs of eukaryotes, prokaryotes, archaebacteria, chloroplasts and mitochondria. One major distinguishing feature between the prokaryotic and eukaryotic 5S RNAs is the number of nucleotide positions between certain universal positions, e.g., prokaryotic 5S RNAs have three positions between the universal positions PuU40 and G44 (using the E. coli numbering system) and eukaryotic 5S RNAs have two. The archaebacterial 5S RNAs appear to resemble the eukaryotic 5S RNAs to varying degrees depending on the species of archaebacteria although all the RNAs conform with the prokaryotic "rule" of chain length between PuU40 and G44. The green plant chloroplast and wheat mitochondrial 5S RNAs appear prokaryotic-like when comparing the number of positions between universal nucleotides. Nucleotide positions common to eukaryotic 5S RNAs have been mapped; in addition, nucleotide sequences, helix lengths and looped-out residues specific to phyla are proposed. Several of the common nucleotides found in the 5S RNAs of metazoan somatic tissue differ in the 5S RNAs of oocytes. These changes may indicate an important functional role of the 5S RNA during oocyte maturation.
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40
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Structural studies of 5 S ribosomal RNAs from a thermophilic fungus, Thermomyces lanuginosus. A comparison of generalized models for eukaryotic 5 S RNAs. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33772-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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41
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Fujiwara H, Ishikawa H. Primary and secondary structures of Tetrahymena and aphid 5.8S rRNAs: structural features of 5.8S rRNA which interacts with the 28S rRNA containing the hidden break. Nucleic Acids Res 1982; 10:5173-82. [PMID: 6815618 PMCID: PMC320863 DOI: 10.1093/nar/10.17.5173] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Tetrahymena 5.8S rRNA is 154 nucleotides long, the shortest so far reported except for the split 5.8S rRNAs of Diptera (m5.8S plus 2S rRNA). In this molecule several nucleotides are deleted in the helix e (GC-rich stem) region. Upon constructing the secondary structure in accordance with "burp-gun" model, the Tetrahymena 5.8S rRNA forms a wide-open "muzzle" of the terminal regions due to both extra nucleotides and several unpaired bases. The aphid 5.8S rRNA consists of 161 nucleotides and can form stable helices in both terminal and helix e regions. As a whole, the secondary structure of Tetrahymena 5.8S rRNA resembles that of Bombyx 5.8S molecule while the aphid 5.8S rRNA shares several structural features with the HeLa 5.8S molecule. Likely, the 5.8S rRNA attached to the 28S rRNA with the hidden break differs in structure from those interacting with the 28S partners without the break. Nucleotide sequences of 5.8S rRNA in insects as well as in protozoans are not so conservative evolutionarily as in vertebrates.
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42
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Clark CG, Gerbi SA. Ribosomal RNA evolution by fragmentation of the 23S progenitor: maturation pathway parallels evolutionary emergence. J Mol Evol 1982; 18:329-36. [PMID: 7120427 DOI: 10.1007/bf01733899] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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43
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Kumazaki T, Hori H, Osawa S. Nucleotide sequence of cytoplasmic 5S ribosomal RNA from Euglena gracilis. J Mol Evol 1982; 18:293-6. [PMID: 6811762 DOI: 10.1007/bf01733894] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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44
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Schnare MN, Gray MW. 3'-Terminal sequence of wheat mitochondrial 18S ribosomal RNA: further evidence of a eubacterial evolutionary origin. Nucleic Acids Res 1982; 10:3921-32. [PMID: 7050913 PMCID: PMC320768 DOI: 10.1093/nar/10.13.3921] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We have determined the sequences of the 3'-terminal approximately 100 nucleotides of [5' -32P]pCp-labeled wheat mitochondrial, wheat cytosol, and E. coli small sub-unit rRNAs. Sequence comparison demonstrates that within this region, there is a substantially greater degree of homology between wheat mitochondrial 18S and E. coli 16S rRNAs than between either of these and wheat cytosol 18S rRNA. Moreover, at a position occupied by 3-methyluridine in E. coli 16S rRNA, the same (or a very similar) modified nucleoside is present in wheat mitochondrial 18S rRNA but not in wheat cytosol 18S rRNA. Further, E. coli 16S and 23S rRNAs hybridize extensively to wheat mitochondrial 18S and 26S rRNA genes, respectively, but wheat cytosol 18S and 26S rRNAs do not. No other mitochondrial system studies to date has provided comparable evidence that a mitochondrial rRNA is more closely related to its eubacterial homolog than is its counterpart in the cytoplasmic compartment of the same cell. The results reported here provide additional support for the view that plant mitochondria are of endosymbiotic, specifically eubacterial, origin.
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45
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Ursi D, Vandenberghe A, De Wachter R. The sequence of the 5.8 S ribosomal RNA of the crustacean Artemia salina. With a proposal for a general secondary structure model for 5.8 S ribosomal RNA. Nucleic Acids Res 1982; 10:3517-30. [PMID: 7099966 PMCID: PMC320728 DOI: 10.1093/nar/10.11.3517] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We report the primary structure of 5.8 S rRNA from the crustacean Artemia salina. The preparation shows length heterogeneity at the 5'-terminus, but consists of uninterrupted RNA chains, in contrast to some insect 5.8 S rRNAs, which consist of two chains of unequal length separated in the gene by a short spacer. The sequence was aligned with those of 11 other 5.8 S rRNAs and a general secondary structure model derived. It has four helical regions in common with the model of Nazar et al. (J. Biol. Chem. 250, 8591-8597 (1975)), but for a fifth helix a different base pairing scheme was found preferable, and the terminal sequences are presumed to bind to 28 S rRNA instead of binding to each other. In the case of yeast, where both the 5.8 S and 26 S rRNA sequences are known, the existence of five helices in 5.8 S rRNA is shown to be compatible with a 5.8 S - 26 S rRNA interaction model.
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46
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De Wachter R, Chen MW, Vandenberghe A. Conservation of secondary structure in 5 S ribosomal RNA: a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable. Biochimie 1982; 64:311-29. [PMID: 6809061 DOI: 10.1016/s0300-9084(82)80436-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The most commonly accepted secondary structure models for 5S RNA differ for molecules of eubacterial origin, where the four-helix model of Fox and Woese is generally cited, and those of eukaryotic origin, where a fifth helix is assumed to exist. We have carefully aligned all available sequences from eukaryotes, eubacteria, chloroplasts, archaebacteria and plant mitochondria. We could thus derive a unified secondary structure model applicable to all 5S RNA sequences known to-date. It contains the five helices already present in the eukaryotic model, extended by additional segments that were not previously assumed to be universally present. One of the helices can be written in two equilibrium forms, which could reflect the existence of a flexible, dynamic structure. For the derivation of the model and the estimation of the free energies we followed a set of rules optimized to predict the tRNA cloverleaf. The stability of the unified model is higher than that of nearly all previously proposed sequence-specific and general models.
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47
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Schnare MN, Gray MW. Nucleotide sequence of an exceptionally long 5.8S ribosomal RNA from Crithidia fasciculata. Nucleic Acids Res 1982; 10:2085-92. [PMID: 7079176 PMCID: PMC320590 DOI: 10.1093/nar/10.6.2085] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In Crithidia fasciculata, a trypanosomatid protozoan, the large ribosomal subunit contains five small RNA species (e, f, g, i, j) in addition to 5S rRNA [Gray, M.W. (1981) Mol. Cell. Biol. 1, 347-357]. The complete primary sequence of species i is shown here to be pAACGUGUmCGCGAUGGAUGACUUGGCUUCCUAUCUCGUUGA ... AGAmACGCAGUAAAGUGCGAUAAGUGGUApsiCAAUUGmCAGAAUCAUUCAAUUACCGAAUCUUUGAACGAAACGG ... CGCAUGGGAGAAGCUCUUUUGAGUCAUCCCCGUGCAUGCCAUAUUCUCCAmGUGUCGAA(C)OH. This sequence establishes that species i is a 5.8S rRNA, despite its exceptional length (171-172 nucleotides). The extra nucleotides in C. fasciculata 5.8S rRNA are located in a region whose primary sequence and length are highly variable among 5.8S rRNAs, but which is capable of forming a stable hairpin loop structure (the "G+C-rich hairpin"). The sequence of C. fasciculata 5.8S rRNA is no more closely related to that of another protozoan, Acanthamoeba castellanii, than it is to representative 5.8S rRNA sequences from the other eukaryotic kingdoms, emphasizing the deep phylogenetic divisions that seem to exist within the Kingdom Protista.
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48
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Küntzel H. Phylogenetic Trees Derived from Mitochondrial, Nuclear, Eubacterial and Archaebacterial rRNA Sequences: Implications on the Origin of Eukaryotes. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s0721-9571(82)80051-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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49
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Erdmann VA. Collection of published 5S and 5.8S RNA sequences and their precursors. Nucleic Acids Res 1982; 10:r93-115. [PMID: 6174939 PMCID: PMC326196 DOI: 10.1093/nar/10.2.762-c] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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50
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Wildeman AG, Nazar RN. Studies on the secondary structure of wheat 5.8 S rRNA. Conformational changes in the A + U-rich stem during ribosome assembly. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 121:357-63. [PMID: 7060553 DOI: 10.1111/j.1432-1033.1982.tb05794.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The nucleotide sequence of wheat (Triticum aestivum) 5.8-S ribosomal RNA has been re-examined using partial chemical degradation with high-temperature sequencing gels and oligonucleotide analysis. The results clarify previously ambiguous residues and add two additional nucleotides, G127 and G135, to the sequence. Estimates of the secondary structure suggest that 5.8-S rRNAs of higher plants differ from previous examples in having more open G + C-rich and A + U-rich stems. S1 ribonuclease digestion was used to probe this secondary structure; the data generally support the 'burp gun' model proposed for all 5.8-S rRNAs but are also consistent with a more open A + U-rich stem. Diethyl pyrocarbonate reactivity was used to probe the topography of this RNA in wheat ribosomes. The results indicate that the G + C-rich and A + U-rich stems are accessible to chemical modification in the wheat ribosome and suggest that the A + U-rich stem undergoes a significant conformational change when the molecule associates into ribosomes.
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