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Vera MI, Rı́os HM, de la Fuente E, Figueroa J, Krauskopf M. Seasonal Acclimatization of the Carp Involves Differential Expression of 5.8S Ribosomal RNA in Pituitary Cells. Comp Biochem Physiol B Biochem Mol Biol 1997. [DOI: 10.1016/s0305-0491(97)00271-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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2
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Kreutzfeldt C, Neumann T, Dierig A. Immunological homologies between ribosomal proteins amongst lower eukaryotes. Curr Genet 1986; 10:537-44. [PMID: 3327609 DOI: 10.1007/bf00447388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polyclonal antibodies were raised against the purified ribosomal proteins L1 and L2, the 5S rRNA binding protein L3, all from Saccharomyces cerevisiae, and against L1 and L2 from Schizosaccharomyces pombe (numbering according to Otaka and Osawa 1981; Otaka et al. 1983, respectively). For clarity prefixes Sc and Sp have been added to the numbering of proteins derived from S. cerevisiae and S. pombe, respectively. Ribosomal proteins from these yeasts and from Kluyveromyces marxianus, Rhodotorula glutinis, the slime mold Dictyostelium discoideum and the protozoan Tetrahymena thermophila were checked for antigenic cross-reactivity by the immunoblot technique. Anti-ScL1 bound to the largest ribosomal proteins of all organisms but not with equal strength. A fast migrating protein band from R. glutinis was also reactive. Anti-ScL2 reacted strongly with L2 or analogous proteins derived exclusively from the yeasts. Anti-ScL3 cross-reacted only with one protein band from K. marxianus, whereas anti-SpL1 cross-reacted with L1 or its analogues from the other organisms, but also with proteins of lower molecular weight. In S. cerevisiae, these proteins are located exclusively on the small ribosomal subunit. L2 or analogous ribosomal proteins of all organisms were recognized by anti-SpL2 but additionally the ribosomal protein YL28 of S. cerevisiae and fast migrating proteins of T. thermophila exhibited anti-SpL2 binding.
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Affiliation(s)
- C Kreutzfeldt
- Institut für Pharmakologie und Toxikologie, Philipps-Universität, Marburg, Federal Republic of Germany
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3
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Nagano K, Harel M. Approaches to a three-dimensional model of E. coli ribosome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1986; 48:67-101. [PMID: 3547502 DOI: 10.1016/0079-6107(86)90001-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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4
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Evstafieva AG, Shatsky IN, Bogdanov AA, Vasiliev VD. Topography of RNA in the ribosome: location of the 5 S RNA residues A39 and U40 on the central protuberance of the 50 S subunit. FEBS Lett 1985; 185:57-62. [PMID: 2581815 DOI: 10.1016/0014-5793(85)80740-7] [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: 01/01/2023]
Abstract
The internal site of 5 S RNA comprising residues A39 and U40 has been localized on the E. coli 50 S ribosomal subunit by immune electron microscopy. It has been found to be located on the interface side of the central protuberance at the position distinctly apart but very close to the position of the 5 S RNA 3'-end providing evidence for a quite compact folded conformation of the 5 S RNA in situ.
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5
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Abstract
We have found a 371-base-pair (bp) repeated DNA element, tau, in Saccharomyces cerevisiae. The ends of tau are composed of a 5-bp inverted repeat, similar in sequence to those reported for the Ty, sigma, copia, and spleen necrosis virus elements. These inverted repeats are flanked by 5-bp direct repeats of a target sequence that occurs only once in an allele that lacks the tau element. This overall structure is characteristic of transposable elements. Like sigma, tau elements have been found (in both orientations) closely associated with tRNA genes (409 and 198 bp from the 5' end, respectively). It is noteworthy that one representative of tau was isolated in a concentric insertion of tau, delta, and sigma.
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6
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Yaguchi M, Rollin CF, Roy C, Nazar RN. The 5S RNA binding protein from yeast (Saccharomyces cerevisiae) ribosomes. An RNA binding sequence in the carboxyl-terminal region. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 139:451-7. [PMID: 6421579 DOI: 10.1111/j.1432-1033.1984.tb08026.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The carboxyl-terminal half (CN2 fragment) of the yeast 5S RNA binding protein (YL3) retains an ability to form homogeneous ribonucleoprotein complexes with RNA although the N-terminal half (CN1) appears to confer specificity for the 5S RNA molecule [Nazar, R.N., Yaguchi, M., Willick, G.E., Rollin, C.F. and Roy, C. (1979) Eur. J. Biochem. 102, 573-582]. The nucleic acid binding site in this fragment was more clearly delineated by cleaving the CN2 fragment with a variety of enzymatic and chemical reagents and further examining the ability of the products to form RNA-peptide complexes. Hot acetic acid treatment produced a 47-residue subfragment (CN2-A1) which originated from the C terminus and continued to form stable ribonucleopeptide complexes. The amino acid sequence of this subfragment was determined to be: -Pro-Ala-Phe-Lys-Pro-Thr-Glu-Lys50-Phe-Thr-Lys-Glu-Gln-Tyr-Ala-Ala -Glu60-Ser-Ly s -Lys-Tyr-Arg-Gln-Thr-Lys-Leu-Ser70-Lys-Gln-Gln-Arg-Ala-Ala-Arg-Val -Ala-Ala80-Ly s -Ile-Ala-Ala-Leu-Ala-Gly-Gln-Gln-COOH, with 12 of the 16 basic residues in the CN2 fragment being present in this binding site. The amino acid sequence of the CN2-A1 fragment bears a limited homology in both amino acid and charge distribution with histone 2B from mammals and with one of the 5S RNA binding proteins (EL25) from Escherichia coli. The results suggest that many protein binding sites for nucleic acids may share common structural features and further support the notion that the single large eukaryotic 5S RNA protein may have evolved through a fusion of genes for the multiple 5S RNA binding proteins in prokaryotes.
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7
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Abstract
Trypanosoma cruzi ribosomal RNA was analyzed electrophoresis. On agarose gels, where both large- and small-size species are grossly fractionable, it revealed two bands in the small-size region. These were similar in size to the mammalian 5.8 S and 5 S species. Increased resolution, however, showed these two bands to be composite. The pseudo 5.8 S band contained three, and the pseudo 5 S two, discretely sized molecules. The ribosomal binding of four of these five novel species is apparently dependent on large ribosomal subunit proteins. One species is hydrogen bonded to the beta species of 24 S ribosomal RNA. The five species were estimated to be 261, 217, 197, 141 and 110 nucleotides long.
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8
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McDougall J, Nazar RN. Tertiary structure of the eukaryotic ribosomal 5 S RNA. Accessibility of phosphodiester bonds to ethylnitrosourea modification. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32566-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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9
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Silberklang M, RajBhandary UL, Lück A, Erdmann VA. Chemical reactivity of E. coli 5S RNA in situ in the 50S ribosomal subunit. Nucleic Acids Res 1983; 11:605-17. [PMID: 6340064 PMCID: PMC325740 DOI: 10.1093/nar/11.3.605] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
E. coli 50S ribosomal subunits were reacted with monoperphthalic acid under conditions in which non-base paired adenines are modified to their 1-N-oxides. 5S RNA was isolated from such chemically reacted subunits and the two modified adenines were identified as A73 and A99. The modified 5S RNA, when used in reconstitution of 50S subunits, yielded particles with reduced biological activity (50%). The results are discussed with respect to a recently proposed three-dimensional structure for 5S RNA, the interaction of the RNA with proteins E-L5, E-L18 and E-L25 and previously proposed interactions of 5S RNA with tRNA, 16S and 23S ribosomal RNAs.
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10
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Maruyama S, Akazaki S, Nitta K, Sugai S. Equilibrium and kinetics of thermal unfolding of yeast 5.8S ribosomal RNA in aqueous salt solutions. Int J Biol Macromol 1983. [DOI: 10.1016/0141-8130(83)90074-0] [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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11
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Erdmann VA, Huysmans E, Vandenberghe A, De Wachter R. Collection of published 5S and 5.8S ribosomal RNA sequences. Nucleic Acids Res 1983; 11:r105-33. [PMID: 6866760 PMCID: PMC325704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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12
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Brimacombe R, Maly P, Zwieb C. The structure of ribosomal RNA and its organization relative to ribosomal protein. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1983; 28:1-48. [PMID: 6348873 DOI: 10.1016/s0079-6603(08)60081-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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13
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Singhal RP, Shaw JK. Prokaryotic and eukaryotic 5 S RNAs: primary sequences and proposed secondary structures. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1983; 28:177-209, 251-2. [PMID: 6348876 DOI: 10.1016/s0079-6603(08)60087-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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14
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15
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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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16
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Goldsbrough PB, Ellis TH, Lomonossoff GP. Sequence variation and methylation of the flax 5S RNA genes. Nucleic Acids Res 1982; 10:4501-14. [PMID: 6290983 PMCID: PMC321107 DOI: 10.1093/nar/10.15.4501] [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: 01/19/2023] Open
Abstract
The complete sequence of the flax 5S DNA repeat is presented. Length heterogeneity is the consequence of the presence or absence of a single direct repeat and the majority of single base changes are transition mutations. No sequence variation has been found in the coding sequence. The extent of methylation of cytosines has been measured at one location in the gene and one in the spacer. The relationship between the observed sequence heterogeneity and the level of methylation is discussed in the context of the operation of a correction mechanism.
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17
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Müller JJ, Damaschun G, Wilhelm P, Welfle H, Pilz I. Comparison of the structures of the native form of rat liver 5S rRNA and yeast tRNAphe: small-angle and wide-angle X-ray scattering study. Int J Biol Macromol 1982. [DOI: 10.1016/0141-8130(82)90057-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Pieler T, Erdmann VA. Three-dimensional structural model of eubacterial 5S RNA that has functional implications. Proc Natl Acad Sci U S A 1982; 79:4599-603. [PMID: 6181508 PMCID: PMC346722 DOI: 10.1073/pnas.79.15.4599] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli 5S RNA and its specific protein complexes were hydrolyzed with the single-strand-specific nuclease S1. Based on the results, a tertiary structural model for E. coli 5S RNA is proposed in which ribosomal proteins E-L5, E-L18, and E-L25 influence the conformation of the RNA. This may be of significance for ribosomal function. Comparison of the proposed E. coli 5S RNA structure with those of 18 other prokaryotic 5S RNAs led to a generalized eubacterial 5S RNA tertiary structure in which the majority of the conserved nucleotides are in non-base-paired regions and several conserved "looped-out" adenines (in E. coli, adenines -52, -53, -57, -58, and -66) are implied to be important for protein recognition or interaction or both.
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19
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del Rey FJ, Donahue TF, Fink GR. sigma, a repetitive element found adjacent to tRNA genes of yeast. Proc Natl Acad Sci U S A 1982; 79:4138-42. [PMID: 6287468 PMCID: PMC346592 DOI: 10.1073/pnas.79.13.4138] [Citation(s) in RCA: 63] [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
sigma is a DNA element of about 340 base pairs (bp) that is repeated many times in the yeast genome. The element has 8-bp inverted repeats at its ends and is flanked by 5-bp direct repeats. The 5-bp repeats are different for each sigma and have no homology with the ends of the sigma sequence. sigma is located 16 or 18 bp from the 5' end of several tRNA genes. Southern analysis of different yeast strains shows that the pattern of hybridization is different even for closely related strains.
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20
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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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21
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Otsuka T, Nomiyama H, Sakaki Y, Takagi Y. Nucleotide sequence of Physarum polycephalum 5.8S rRNA gene and its flanking regions. Nucleic Acids Res 1982; 10:2379-85. [PMID: 6283479 PMCID: PMC320616 DOI: 10.1093/nar/10.7.2379] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nucleotide sequence of Physarum polycephalum 5.8S rRNA gene and its flanking regions has been determined. The homologies of the 5.8S rRNA sequence with those of Saccharomyces, Chlamydomonas and Xenopus were 56%, 50% and 52%, respectively. In spite of these relatively low homologies, its possible secondary structure was very similar to those of other species.
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22
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Lee JC, Henry B. Binding of rat ribosomal proteins to yeast 5.8S ribosomal ribonucleic acid. Nucleic Acids Res 1982; 10:2199-207. [PMID: 7045808 PMCID: PMC320603 DOI: 10.1093/nar/10.7.2199] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
5.8 S RNA-protein complexes were prepared using purified yeast 5.8 S RNA and proteins from the large ribosomal subunit of rat liver. Formation of such hybrid complexes, as measured by Millipore filtration, was dependent on protein concentration. Binding of proteins to the RNA could approach saturation. Such complexes were isolated from sucrose density gradient centrifugation and shown to contain proteins L6, L8, L19, L35 and L35a. These proteins were identified by their molecular weights on polyacrylamide gels containing dodecylsulfate and their mobilities on two dimensional polyacrylamide gels.
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23
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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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24
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Kawata Y, Ishikawa H. Nucleotide sequence and thermal property of 5S rRNA from the elder aphid. Acyrthosiphon magnoliae. Nucleic Acids Res 1982; 10:1833-40. [PMID: 6804932 PMCID: PMC320574 DOI: 10.1093/nar/10.6.1833] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The nucleotide sequence of 5S rRNA from the elder aphid. Acyrthosiphon magnoliae was determined by using postlabeling sequencing techniques. The aphid 5S rRNA consists of 120 nucleotides and the sequence differs from those of Bombyx and Drosophila 5S rRNAs in 14 and 16 positions, respectively. A secondary structure model based on the sequence has two distinctive features : the helix I is shorter and the total free energy lower. Judging from the thermal profile, the aphid 5S rRNA likely assumes a conformation somewhat different from those of the other two insects.
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25
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26
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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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27
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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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28
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Auron PE, Rindone WP, Vary CP, Celentano JJ, Vournakis JN. Computer-aided prediction of RNA secondary structures. Nucleic Acids Res 1982; 10:403-19. [PMID: 6174937 PMCID: PMC326142 DOI: 10.1093/nar/10.1.403] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A brief survey of computer algorithms that have been developed to generate predictions of the secondary structures of RNA molecules is presented. Two particular methods are described in some detail. The first utilizes a thermodynamic energy minimization algorithm that takes into account the likelihood that short-range folding tends to be favored over long-range interactions. The second utilizes an interactive computer graphic modelling algorithm that enables the user to consider thermodynamic criteria as well as structural data obtained by nuclease susceptibility, chemical reactivity and phylogenetic studies. Examples of structures for prokaryotic 16S and 23S ribosomal RNAs, several eukaryotic 5S ribosomal RNAs and rabbit beta-globin messenger RNA are presented as case studies in order to describe the two techniques. Anm argument is made for integrating the two approaches presented in this paper, enabling the user to generate proposed structures using thermodynamic criteria, allowing interactive refinement of these structures through the application of experimentally derived data.
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29
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Abstract
Minimal mutation trees, and almost minimal trees, are constructed from two data sets, one of phenylalanine tRNA sequences, and the other of 5S RNA sequences, from a diverse range of organisms. The two sets of results are mutually consistent. Trees representing previous evolutionary hypotheses are compared using a total weighted mutational distance criterion. The importance of sequence data from relatively little-studed phylogenetic lines is stressed. A procedure is illustrated which circumvents the computational difficulty of evaluating the astronomically large number of possible trees, without resorting to suboptimal methods.
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30
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Galli G, Hofstetter H, Birnstiel ML. Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. Nature 1981; 294:626-31. [PMID: 7312050 DOI: 10.1038/294626a0] [Citation(s) in RCA: 407] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The split promoter sequences of a tRNALeuCUG gene of Xenopus laevis have been mapped to nucleotides 13-20 and 51-64 of the tRNALeu coding sequences. The sequences closely coincide with two conserved sequence blocks present in all eukaryotic tRNA genes. The two conserved sequence blocks were found to be exchangeable between tRNA genes as chimaeric tRNAMet--tRNALeu genes proved transcriptionally active. Furthermore, two prokaryotic tRNA genes exhibiting strong homologies with the two blocks yielded specific transcripts when tested in an eukaryotic transcriptional system.
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31
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Peattie DA, Douthwaite S, Garrett RA, Noller HF. A "bulged" double helix in a RNA-protein contact site. Proc Natl Acad Sci U S A 1981; 78:7331-5. [PMID: 7038676 PMCID: PMC349260 DOI: 10.1073/pnas.78.12.7331] [Citation(s) in RCA: 113] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The binding of ribosomal protein L18 affects specific nucleotides in Escherichia coli 5S RNA as detected by dimethyl sulfate alkylation and RNase A digestion of the 5S-L18 complex. Most of the affected nucleotides are clustered and localize a site of RNA-protein interaction in and around the defined central helix [Fox, G. E. & Woese, C. (1975) Nature (London) 256, 505-507] of 5S RNA. Chemical carbethoxylation of the native 5S RNA with diethyl pyrocarbonate shows that a striking feature of this region is an unstacked adenosine residue at position 66. We propose that this residue exists as a singly bulged nucleotide extending the Fox and Woese central helix by two base pairs in the E. coli sequence (to positions 16-23/60-68) as well as in each of 61 (prokaryotic and eukaryotic) aligned 5S RNA sequences. In each case, the single bulged nucleotide is at the relative position of adenosine-66 in the RNA sequences. The presence of this putative bulged nucleotide appears to have been conserved in 5S RNA sequences throughout evolution, and its identity varies with major phylogenetic divisions. This residue is likely involved in specific 5S RNA-protein recognition or interaction in prokaryotic and eukaryotic ribosomes. The uridine-65 to adenosine-66 internucleotide bond is protected from RNase A digestion in the complex, and carbethoxylation of E. coli adenosine-66 prior to L18 binding affects formation of a stable RNA-protein complex. Thus, we identify a region of E. coli 5S RNA protected by the ribosomal protein L18 and propose that it contains a bulged nucleotide residue important in stable formation of this RNA-protein complex. This bulged residue appears to be evolutionarily conserved and phylogenetically defined in 5S RNA sequences in general, and consideration of other known RNA-protein binding sites shows that such a "bulged helix" may be a common feature of RNA-protein contact sites.
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32
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The nucleotide sequence of a minor 5 S RNA species from Lactobacillus viridescens. FEBS Lett 1981. [DOI: 10.1016/0014-5793(81)80965-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Kumagai I, Digweed M, Erdmann VA, Watanabe K, Oshima T. The nucleotide sequence of 5S rRNA from an extreme thermophile, Thermus thermophilus HB8. Nucleic Acids Res 1981; 9:5159-62. [PMID: 6171775 PMCID: PMC327506 DOI: 10.1093/nar/9.19.5159] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Using 3'- and 5'-end labelling sequencing techniques, the following primary structure for Thermusthermophilus HB8 5S RNA could be determined: pAA (U) CCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAACGCGCCAGCGCC GAUGGUACUGGCGGACGACCGCUGGGAGAGUAGGUCGGUGCGGGGGA (OH). This sequence is most similar to Thermusaquaticus 5S RNA with which it shows 85% homology.
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34
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Diels L, De Baere R, Vandenberghe A, De Wachter R. The sequence of 5S ribosomal RNA of the crustacean Artemia salina. Nucleic Acids Res 1981; 9:5141-4. [PMID: 7312626 PMCID: PMC327504 DOI: 10.1093/nar/9.19.5141] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The primary structure of the 5 S rRNA isolated from the cryptobiotic cysts of the brine shrimp Artemia salina is pACCAACGGCCAUACCACGUUGAAAGUACCCAGUCUCGUCAGAUCCUGGAAGUCACACAACGUCGGGCCCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGGGUGCUGUUGGCAU (OH).
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MacKay RM, Doolittle WF. Nucleotide sequences of Acanthamoeba castellanii 5S and 5.8S ribosomal ribonucleic acids: phylogenetic and comparative structural analyses. Nucleic Acids Res 1981; 9:3321-34. [PMID: 7279665 PMCID: PMC327354 DOI: 10.1093/nar/9.14.3321] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Sequences of 5S and 5.8S rRNAs of the amoeboid protist Acanthamoeba castellanii have been determined by gel sequencing of terminally-labeled RNAs which were partially degraded with chemical reagents or ribonucleases. The sequence of the 5S rRNA is (formula, see text). This sequence is compared to eukaryotic 5S rRNA sequences previously published and fitted to a secondary structure model which incorporates features of several previously proposed models. All reported eukaryotic 5S rRNAs fit this model. The sequence of the 5.8S rRNA is (formula, see text). This sequence does not fit parts of existing secondary structure models for 5.8S rRNA, and we question the significance of such models.
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Spencer DF, Bonen L, Gray MW. Primary sequence of wheat mitochondrial 5S ribosomal ribonucleic acid: functional and evolutionary implications. Biochemistry 1981; 20:4022-9. [PMID: 7284306 DOI: 10.1021/bi00517a011] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Using the procedures of Donis-Keller et al. [Donis-Keller, H., Maxam, A. M., & Gilbert, W. (1977) Nucleic Acids Res. 4, 2527--2538 (1977)] and Peattie [Peattie, D. A. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 1760--1764], we have determined the nucleotide sequence of wheat mitochondrial 5S ribosomal ribonucleic acid (rRNA). This sequence [Formula: see text] is the first to be reported for a plant mitochondrial RNA. A highly conserved region (underlined) readily identifies the molecule as a structural homologue of other 5S rRNAs, as do potential base-paired regions which are characteristic of all known (prokaryotic, chloroplast, eukaryotic cytosol) 5S rRNA sequences. However, when assessed in terms of those structural features which distinguish prokaryotic from eukaryotic 5S rRNAs, wheat mitochondrial 5S rRNA cannot be classified readily as one or the other but instead displays characteristics of both types. In addition, the mitochondrial 5S rRNA has several unusual features, including (i) a variable number (two to three) of A residues at both the 5' and 3' ends, (ii) a unique sequence (CGACC, italic) in place of the prokaryotic sequence (CGAAC) which has been postulated to interact with aminoacyl-tRNA during translation, and (iii) a novel sequence, AUAUAUAU, immediately following the highly conserved sequence. In terms of overall primary sequence, wheat mitochondrial and cytosol 5S rRNAs seem to be slightly more divergent from each other than either is from Escherichia coli 5S rRNA, with which they are about equally homologous. From these observations, we propose that wheat mitochondrial 5S rRNA represents a distinct class of 5S rRNA. Our observations raise a number of questions about the evolutionary origin and functional role(s) of plant mitochondrial 5S rRNA.
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Delihas N, Andersen J, Sprouse HM, Dudock B. The nucleotide sequence of the chloroplast 5S ribosomal RNA from spinach. Nucleic Acids Res 1981; 9:2801-5. [PMID: 7279661 PMCID: PMC326894 DOI: 10.1093/nar/9.12.2801] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Spinacia oleracia cholorplast 5S ribosomal RNA was end-labeled with [32P] and the complete nucleotide sequence was determined. The sequence is: pUAUUCUGGUGUCCUAGGCGUAGAGGAACCACACCAAUCCAUCCCGAACUUGGUGGUUAAACUCUACUGCGGUGACGAU ACUGUAGGGGAGGUCCUGCGGAAAAAUAGCUCGACGCCAGGAUGOH. This sequence can be fitted to the secondary structural model proposed for prokaryotic 5S ribosomal RNAs by Fox and Woese (1). However, the lengths of several single- and double-stranded regions differ from those common to prokaryotes. The spinach chloroplast 5S ribosomal RNA is homologous to the 5S ribosomal RNA of Lemna chloroplasts with the exception that the spinach RNA is longer by one nucleotide at the 3' end and has a purine base substitution at position 119. The sequence of spinach chloroplast 5S RNA is identical to the chloroplast 5S ribosomal RNA gene of tobacco. Thus the structures of the chloroplast 5S ribosomal RNAs from some of the higher plants appear to be almost totally conserved. This does not appear to be the case for the higher plant cytoplasmic 5S ribosomal RNAs.
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Butler MH, Wall SM, Luehrsen KR, Fox GE, Hecht RM. Molecular relationships between closely related strains and species of nematodes. J Mol Evol 1981; 18:18-23. [PMID: 7334524 DOI: 10.1007/bf01733207] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Electrophoretic comparisons have been made for 24 enzymes in the Bergerac and Bristol strains of Caenorhabditis elegans and the related species, Caenorhabditis briggsae. No variation was detected between the two strains of C. elegans. In contrast, the two species, C. elegans and C. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined for C. elegans and found to be identical to that from C. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years. The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein changes.
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