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Ji GE, Orlowski M. Primary and secondary structure of the 25S rRNA from the dimorphic fungus Mucor racemosus. Curr Genet 1990; 17:499-506. [PMID: 2390785 DOI: 10.1007/bf00313078] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A 9.76 Kb ribosomal DNA repeat unit from the nuclear genome of the dimorphic fungus Mucor racemosus (Zygomycetes) was identified using a hybridization probe from the yeast Saccharomyces cerevisiae (Ascomycetes). This material was cloned in Escherichia coli plasmids as four overlapping pieces and mapped with respect to cleavage sites for 12 restriction endonucleases. The nucleotide sequence of the complete 25S rRNA gene and flanking regions was determined. The 5' and 3' ends of the structural gene were identified by comparison with the published sequence for the S. cerevisiae gene. The Mucor gene was found to possess 3469 bp and have a GC content of 42.8%. It was compared with the homologous gene from several other eukaryotes and found to be most similar to that from Saccharomyces. A potential secondary structure of the putative RNA transcript consistent with the structures proposed for the E. coli and Saccharomyces molecules was constructed by computer modelling.
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Affiliation(s)
- G E Ji
- Department of Microbiology, Louisiana State University, Baton Rouge 70803-1715
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52
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Engberg J, Nielsen H, Lenaers G, Murayama O, Fujitani H, Higashinakagawa T. Comparison of primary and secondary 26S rRNA structures in two Tetrahymena species: evidence for a strong evolutionary and structural constraint in expansion segments. J Mol Evol 1990; 30:514-21. [PMID: 2115930 DOI: 10.1007/bf02101107] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have determined the nucleotide sequence of the 26S large subunit (LSU) rRNA genes for two Tetrahymena species, T. thermophila and T. pyriformis. The inferred rRNA sequences are presented in their most probable secondary structures based on compensatory mutations, energy, and conservation criteria. The majority of the nucleotide changes between the two Tetrahymena LSU rRNAs and the positions of a relatively large deletion and of the processing cleavage sites resulting in the generation of the hidden break are all located within the so-called divergent domains or expansion segments. These are regions within the common core of secondary structure where expansions have taken place during the evolution of the rRNA of higher eukaryotes. The dispensable nature of some of the expansion segments has been taken as evidence of their non-functionality. However, our data show that a considerable selective constraint has operated to preserve the secondary structure of these segments. Especially in the case of the D2 and D8 segments, the presence of a considerable number of compensatory base changes suggests that the secondary structure of these regions is of functional importance. Alternatively, these expansion segments may have maintained characteristic folding patterns because only such structures are being tolerated within otherwise functionally important regions.
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Affiliation(s)
- J Engberg
- Department of Biochemistry B, Panum Institute, University of Copenhagen, Denmark
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53
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Michot B, Qu LH, Bachellerie JP. Evolution of large-subunit rRNA structure. The diversification of divergent D3 domain among major phylogenetic groups. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 188:219-29. [PMID: 2138538 DOI: 10.1111/j.1432-1033.1990.tb15393.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
During evolution, the potential for sequence (and length) variation of large-subunit rRNA has been mostly restricted over 12 divergent domains (termed D1-D12) interspersed along the molecule. Here, we have focused our attention onto the D3 divergent domain, through a detailed analysis of its pattern of variation in the phylogeny, both in terms of primary and secondary structures. We have systematically compared all the procaryotic and eucaryotic sequences published so far (i.e. 36 species), together with a series of 10 additional eucaryotic specimens, which were determined by direct RNA sequencing. Secondary structures supported by comparative evidence have been derived for archaebacteria, eubacteria and eucaryotes respectively, which shows that the D3 domain contains a subset of universally conserved structural features interspersed with four variable subdomains. Within the four portions where a structural diversification has taken place, elementary structures specific of large phylogenetic groups can be identified. Remarkably such diversified structures appear to be preserved despite sequence divergence, suggesting they correspond to functionally important structures. Accordingly, the mode of sequence variation of the D3 domain suggests this region of the molecule may encode elementary functions of rRNA which could have significantly diversified during the evolution of the major groups of organisms.
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Affiliation(s)
- B Michot
- Centre de Recherches de Biochimie et de Génétique Cellulaires du Centre National de la Recherche Scientifique, Université Paul-Sabatier, Toulouse, France
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54
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Gonzalez IL, Chambers C, Gorski JL, Stambolian D, Schmickel RD, Sylvester JE. Sequence and structure correlation of human ribosomal transcribed spacers. J Mol Biol 1990; 212:27-35. [PMID: 2319598 DOI: 10.1016/0022-2836(90)90302-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the sequences of the transcribed spacers of human rRNA that now allow us to piece together the entire primary transcript sequence of approximately 13.3 x 10(3) base-pairs. Comparison of transcribed spacer sequences with those of variable regions of rRNA and with those of the non-transcribed spacers supports the hypothesis that the variable regions are descended from transcribed spacers. Nucleotide sequence-derived secondary structures for the 5' external transcribed spacer and for internal transcribed spacers 1 and 2 match both the sizes and shapes of the structures that were visualized 15 years ago on electron micrographs. Parts of these structures are conserved in mammals and may be related to transcript processing.
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Affiliation(s)
- I L Gonzalez
- Hahnemann University, Department of Pathology, Philadelphia, PA 19102
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55
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Burgin AB, Parodos K, Lane DJ, Pace NR. The excision of intervening sequences from Salmonella 23S ribosomal RNA. Cell 1990; 60:405-14. [PMID: 2406020 DOI: 10.1016/0092-8674(90)90592-3] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Novel, approximately 90 bp intervening sequences (IVs) were discovered within the 23S rRNA genes of S. typhimurium and S. arizonae. These non-rRNA sequences are transcribed and then excised during rRNA maturation. The rRNA fragments that result from the excision of the extra sequences are not religated. This results in fragmented 23S rRNAs. The excision of one IVS was shown to be catalyzed in vivo and in vitro by ribonuclease III. These IVSs are highly volatile evolutionarily, sometimes occurring in only some of the multiple rRNA operons of a particular cell. The sporadic nature of the occurrence of fragmented rRNAs among closely related organisms argues that such fragmentation is a derived state, not a primitive one. Possible sources of these IVSs, their parallels with internal transcribed spacers and introns in eukaryotes, and their possible roles in the evolutionary process are discussed.
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MESH Headings
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- DNA, Ribosomal/genetics
- Endoribonucleases
- Escherichia coli/genetics
- Escherichia coli Proteins
- Genes, Bacterial
- Molecular Sequence Data
- Oligonucleotide Probes
- Plasmids
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/isolation & purification
- Ribonuclease III
- Salmonella/genetics
- Salmonella arizonae/genetics
- Salmonella typhimurium/genetics
- Transcription, Genetic
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Affiliation(s)
- A B Burgin
- Department of Biology, Indiana University, Bloomington 47405
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56
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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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57
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Purugganan MD. The fractal nature of RNA secondary structure. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1989; 76:471-3. [PMID: 2479842 DOI: 10.1007/bf00366226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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58
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Auer J, Spicker G, Böck A. Organization and structure of the Methanococcus transcriptional unit homologous to the Escherichia coli "spectinomycin operon". Implications for the evolutionary relationship of 70 S and 80 S ribosomes. J Mol Biol 1989; 209:21-36. [PMID: 2530355 DOI: 10.1016/0022-2836(89)90167-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
By means of an immunological approach and a subsequent chromosome-walking strategy a chromosomal region encoding ribosomal proteins in the archaebacterium Methanococcus vannielii was cloned. The determination of the nucleotide sequence of the 7.8 x 10(3) base DNA fragment revealed the existence of 14 putative ribosomal protein genes and two unidentified open reading frames. They are organized in a transcriptional unit that is very similar to the Escherichia coli "spectinomycin operon" in respect of both gene composition and gene order. The Methanococcus transcriptional unit contains, in addition to those genes whose products have a homologue in the E. coli operon, three genes whose products share sequence similarity with eukaryotic 80 S but not with eubacterial ribosomal proteins. The Methanococcus ribosomal proteins almost exclusively exhibit a higher sequence similarity to eukaryotic 80 S ribosomal proteins than to those of eubacteria and many of them have a size intermediate between those of their eukaryotic and eubacterial homologues. These results are discussed in terms of a hypothesis that implies that the recent eubacterial ribosome developed by a "minimization" process from a more complex organelle and that the archaebacterial ribosome has maintained features of this ancestor.
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Affiliation(s)
- J Auer
- Lehrstuhl für Mikrobiologie der Universität, München, F.R.G
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59
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Vaidya AB, Akella R, Suplick K. Sequences similar to genes for two mitochondrial proteins and portions of ribosomal RNA in tandemly arrayed 6-kilobase-pair DNA of a malarial parasite. Mol Biochem Parasitol 1989; 35:97-107. [PMID: 2549417 DOI: 10.1016/0166-6851(89)90112-6] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Erythrocytic stages of mammalian malarial parasites contain acristate mitochondria whose functions are not well understood. Moreover, little is known about the genome of these organelles. We have previously reported that all species of malarial parasites examined contain highly conserved, tandemly arrayed DNA with a unit length of about 6.0 kb that is transcribed into discrete RNA molecules in erythrocytic stages. We now report the complete DNA sequence of the 5984-bp repeating unit of Plasmodium yoelii, a rodent parasite. Two slightly overlapping regions transcribed into large RNA molecules were found to have significant DNA and protein sequence similarity with mitochondrion-coded proteins, cytochrome c oxidase subunit I and cytochrome b. Significant sequence similarity with other mitochondrial protein genes could not be detected. Ribosomal RNA (rRNA)-like genes were not detected in this sequence either. However, two regions, 82 and 50 nucleotides long, specified by different strands, were found to have extensive similarity with the highly conserved central loop of the peptidyl transferase domain of the large rRNA of Escherichia coli, mitochondria, and chloroplasts. Compensatory nucleotide substitutions were present in these regions, so that the predicted secondary structure was not affected. Functional utilization of these regions, if it exists, could argue for a trans-associative origin of rRNA. In organization, size and sequence, the tandem arrays of 6.0 kb malarial DNA appear to be a very unusual form of mitochondrial DNA.
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Affiliation(s)
- A B Vaidya
- Department of Microbiology and Immunology, Hahnemann University, Philadelphia, PA 19102-1192
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60
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de Lanversin G, Jacq B. Sequence and secondary structure of the central domain of Drosophila 26S rRNA: a universal model for the central domain of the large rRNA containing the region in which the central break may happen. J Mol Evol 1989; 28:403-17. [PMID: 2501502 DOI: 10.1007/bf02603076] [Citation(s) in RCA: 18] [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
An 890-bp sequence from the central region of Drosophila melanogaster 26S ribosomal DNA (rDNA) has been determined and used in an extensive comparative analysis of the central domain of the large subunit ribosomal RNA (lrRNA) from prokaryotes, organelles, and eukaryotes. An alignment of these different sequences has allowed us to precisely map the regions of the central domain that have highly diverged during evolution. Using this sequence comparison, we have derived a secondary structure model of the central domain of Drosophila 26S ribosomal RNA (rRNA). We show that a large part of this model can be applied to the central domain of lrRNA from prokaryotes, eukaryotes, and organelles, therefore defining a universal common structural core. Likewise, a comparative study of the secondary structure of the divergent regions has been performed in several organisms. The results show that, despite a nearly complete divergence in their length and sequence, a common structural core is also present in divergent regions. In some organisms, one or two of the divergent regions of the central domain are removed by processing events. The sequence and structure of these regions (fragmentation spacers) have been compared to those of the corresponding divergent regions that remain part of the mature rRNA in other species.
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Affiliation(s)
- G de Lanversin
- Laboratoire de Génétique et Biologie Cellulaires, CNRS, Marseille, France
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61
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62
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Gonzalez IL, Sylvester JE, Schmickel RD. Human 28S ribosomal RNA sequence heterogeneity. Nucleic Acids Res 1988; 16:10213-24. [PMID: 3194198 PMCID: PMC338847 DOI: 10.1093/nar/16.21.10213] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
DNA sequencing of several cloned human 28S ribosomal RNA gene fragments has revealed sequence heterogeneity (1) but it was not clear whether these are inactive pseudogenes or are active genes that are transcribed and represented in ribosomes. S1 nuclease analysis allowed us to examine the population of ribosomal RNA molecules of a cell, and we found that 28S rRNA is a heterogeneous assortment of molecules in both mono- and polysomal preparations. Sequence variation, although largely concentrated in variable regions of the molecule, apparently also occurs in the conserved regions.
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Affiliation(s)
- I L Gonzalez
- Department of Human Genetics, University of Pennsylvania, Philadelphia 19104
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63
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Vahidi H, Curran J, Nelson DW, Webster JM, McClure MA, Honda BM. Unusual sequences, homologous to 5S RNA, in ribosomal DNA repeats of the nematode Meloidogyne arenaria. J Mol Evol 1988; 27:222-7. [PMID: 3138424 DOI: 10.1007/bf02100078] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
There are sequences homologous to 5S ribosomal RNA in the ribosomal DNA (rDNA) repeats of the plant-parasitic nematode Meloidogyne arenaria. This is surprising, because in all other higher eukaryotes studied to date, the genes for 5S RNA are unlinked to and distinct from a tandem rDNA repeat containing the genes for 18S, 5.8S, and 28S ribosomal RNA. Previously, only prokaryotes and certain "lower eukaryotes" (protozoa and fungi) had been found to have both the larger rRNAs and 5S rRNA represented within a single DNA repeat. This has raised questions on the organization of these repeats in the earliest cell (progenote), and on subsequent evolutionary relationships between pro- and eukaryotes. Evidence is presented for rearrangements and deletions within Meloidogyne rDNA. The unusual life cycles (different levels of ploidy, reproduction by meiotic and mitotic parthenogenesis) of members of this genus might allow rapid fixation of any variants with introduced 5S RNA sequences. The 5S RNA sequences in Meloidogyne rDNA may not be expressed, but their presence raises important questions as to the evolutionary origins and stability of repeat gene families.
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Affiliation(s)
- H Vahidi
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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64
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Raué HA, Klootwijk J, Musters W. Evolutionary conservation of structure and function of high molecular weight ribosomal RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1988; 51:77-129. [PMID: 3076243 DOI: 10.1016/0079-6107(88)90011-9] [Citation(s) in RCA: 126] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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