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Mlinarec J, Boštjančić LL, Malenica N, Jurković A, Boland T, Yakovlev SS, Besendorfer V. Structure and Methylation of 35S rDNA in Allopolyploids Anemone multifida (2 n = 4 x = 32, BBDD) and Anemone baldensis (2 n = 6 x = 48, AABBDD) and Their Parental Species Show Evidence of Nucleolar Dominance. FRONTIERS IN PLANT SCIENCE 2022; 13:908218. [PMID: 35874014 PMCID: PMC9296772 DOI: 10.3389/fpls.2022.908218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/07/2022] [Indexed: 05/26/2023]
Abstract
Transcriptional silencing of 35S rDNA loci inherited from one parental species is occurring relatively frequently in allopolyploids. However, molecular mechanisms by which it is selected for transcriptional silencing remain unclear. We applied NGS, silver staining and bisulfite sequencing to study the structure, expression and methylation landscape of 35S rDNA in two allopolyploids of common origin, allotetraploid Anemone multifida (2n = 4x = 32, genome composition BBDD) and allohexaploid A. baldensis (2n = 6x = 48, AABBDD), and their genome donors, A. sylvestris (2n = 16, AA), A. cylindrica (2n = 16, BB) and A. parviflora (2n = 16, DD). The size of the recovered 35S rDNA units varied from 10,489 bp in A. cylindrica to 12,084 bp in A. sylvestris. Anemone showed an organization typical of most ribosomal 35S rDNA composed of NTS, ETS, rRNA genes, TTS and TIS with structural features of plant IGS sequences and all functional elements needed for rRNA gene activity. The NTS was more variable than the ETS and consisted of SRs which are highly variable among Anemone. Five to six CpG-rich islands were found within the ETS. CpG island located adjacent to the transcription initiation site (TIS) was highly variable regarding the sequence size and methylation level and exhibited in most of the species lower levels of methylation than CpG islands located adjacent to the 18S rRNA gene. Our results uncover hypomethylation of A. sylvestris- and A. parviflora-derived 35S rDNA units in allopolyploids A. multifida and A. baldensis. Hypomethylation of A. parviflora-derived 35S rDNA was more prominent in A. baldensis than in A. multifida. We showed that A. baldensis underwent coupled A. sylvestris-derived 35S rDNA array expansion and A. parviflora-derived 35S rDNA copy number decrease that was accompanied by lower methylation level of A. sylvestris-derived 35S rDNA units in comparison to A. parviflora-derived 35S rDNA units. These observations suggest that in A. baldensis nucleolar dominance is directed toward A. sylvestris-derived chromosomes. This work broadens our current knowledge of the 35S rDNA organization in Anemone and provides evidence of the progenitor-specific 35S rDNA methylation in nucleolar dominance.
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Affiliation(s)
| | - Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
- Department of Computer Science, ICube, UMR 7357, CNRS, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, Strasbourg, France
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Todd Boland
- Memorial University of Newfoundland’s Botanical Gardens, St. John’s, NL, Canada
| | - Sonja Siljak Yakovlev
- CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
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Characterization analysis of the 35S rDNA intergenic spacers in Erianthus arundinaceus. Gene 2019; 694:63-70. [PMID: 30716441 DOI: 10.1016/j.gene.2019.01.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 11/21/2022]
Abstract
The 35S ribosomal DNA (rDNA) units that occur in tandem repeat are separated by an intergenic spacer (IGS) that plays an important role in rRNA transcription. Moreover, IGS is an important molecular marker for evolutionary research in plants. In the present study, the IGS sequence of Erianthus arundinaceus was isolated and sequenced for the first time. Structure analysis indicated the entire IGS sequence of three typical E. arundinaceus genotypes was highly conserved, with approximately 3087 bp and 67.1% mean GC content. The putative transcription termination, and initiation sites as well as a large number of methylation sites were found to be present in the IGS of E. arundinaceus compared to other plants. The phylogenic tree constructed using the E. arundinaceus IGS sequence showed that Miscanthus sinensis var. glaber was genetically close to Saccharum spp. while E. arundinaceus was close to Imperata cylindrica. Moreover, fluorescent in situ hybridization revealed that IGS and pTa71 probes had the same locus at nucleolar organizer regions. Taken together, this work enhances our current understanding of the organization of IGS in E. arundinaceus and provides a molecular evidence for an evolutionary relationship between Saccharum spp., E. arundinaceus, I. cylindrica and M. sinensis var. glaber.
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Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of Brassica oleracea L. var. capitata. Int J Mol Sci 2015; 16:28783-99. [PMID: 26633391 PMCID: PMC4691072 DOI: 10.3390/ijms161226125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 11/24/2022] Open
Abstract
Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were quite similar in length. The 45S IGSs were found to follow Mendelian inheritance in a population of 15 F1s and their 30 inbred parental lines, which suggests that these sequences could be useful for development of new breeding tools. In addition, this study represents the first report of intra-specific (within subspecies) variation of the 45S IGS in B. oleracea.
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Zentgraf U, King K, Hemleben V. Repetitive sequences are valuable as molecular markers in studies of phylogenetic relationships within the genusCucumis. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/j.1438-8677.1992.tb00509.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- U. Zentgraf
- Department of Genetics; Biological Institute, University of Tübingen, Auf der Morgenstelle 28; W-7400 Tübingen Germany
| | - K. King
- Department of Genetics; Biological Institute, University of Tübingen, Auf der Morgenstelle 28; W-7400 Tübingen Germany
| | - V. Hemleben
- Department of Genetics; Biological Institute, University of Tübingen, Auf der Morgenstelle 28; W-7400 Tübingen Germany
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Dai Y, Wang QW, He S, Zhang Z, Gao C. Correlation of ECR1 A3650G Polymorphism with Neonatal Respiratory Distress Syndrome. Genet Test Mol Biomarkers 2015; 19:18-23. [PMID: 25494101 DOI: 10.1089/gtmb.2014.0192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Ying Dai
- Department of Pediatrics, Huaihe Hospital, Henan University, Kaifeng, Henan, People's Republic of China
| | - Qi-Wei Wang
- Department of Pediatrics, Huaihe Hospital, Henan University, Kaifeng, Henan, People's Republic of China
| | - Shu He
- Department of Pediatrics, Huaihe Hospital, Henan University, Kaifeng, Henan, People's Republic of China
| | - Zhao Zhang
- Department of Pediatrics, Huaihe Hospital, Henan University, Kaifeng, Henan, People's Republic of China
| | - Chao Gao
- Department of Medicine and Equipment, Huaihe Hospital, Henan University, Kaifeng, Henan, People's Republic of China
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Inácio V, Rocheta M, Morais-Cecílio L. Molecular organization of the 25S-18S rDNA IGS of Fagus sylvatica and Quercus suber: a comparative analysis. PLoS One 2014; 9:e98678. [PMID: 24893289 PMCID: PMC4043768 DOI: 10.1371/journal.pone.0098678] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 05/05/2014] [Indexed: 01/28/2023] Open
Abstract
The 35S ribosomal DNA (rDNA) units, repeated in tandem at one or more chromosomal loci, are separated by an intergenic spacer (IGS) containing functional elements involved in the regulation of transcription of downstream rRNA genes. In the present work, we have compared the IGS molecular organizations in two divergent species of Fagaceae, Fagus sylvatica and Quercus suber, aiming to comprehend the evolution of the IGS sequences within the family. Self- and cross-hybridization FISH was done on representative species of the Fagaceae. The IGS length variability and the methylation level of 18 and 25S rRNA genes were assessed in representatives of three genera of this family: Fagus, Quercus and Castanea. The intergenic spacers in Beech and Cork Oak showed similar overall organizations comprising putative functional elements needed for rRNA gene activity and containing a non-transcribed spacer (NTS), a promoter region, and a 5′-external transcribed spacer. In the NTS: the sub-repeats structure in Beech is more organized than in Cork Oak, sharing some short motifs which results in the lowest sequence similarity of the entire IGS; the AT-rich region differed in both spacers by a GC-rich block inserted in Cork Oak. The 5′-ETS is the region with the higher similarity, having nonetheless different lengths. FISH with the NTS-5′-ETS revealed fainter signals in cross-hybridization in agreement with the divergence between genera. The diversity of IGS lengths revealed variants from ∼2 kb in Fagus, and Quercus up to 5.3 kb in Castanea, and a lack of correlation between the number of variants and the number of rDNA loci in several species. Methylation of 25S Bam HI site was confirmed in all species and detected for the first time in the 18S of Q. suber and Q. faginea. These results provide important clues for the evolutionary trends of the rDNA 25S-18S IGS in the Fagaceae family.
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Affiliation(s)
- Vera Inácio
- Centre for Botany Applied to Agriculture (CBAA), Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - Margarida Rocheta
- Centre for Botany Applied to Agriculture (CBAA), Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - Leonor Morais-Cecílio
- Centre for Botany Applied to Agriculture (CBAA), Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
- * E-mail:
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Garcia S, Crhák Khaitová L, Kovařík A. Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence. BMC PLANT BIOLOGY 2012; 12:95. [PMID: 22716941 PMCID: PMC3409069 DOI: 10.1186/1471-2229-12-95] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 06/20/2012] [Indexed: 05/09/2023]
Abstract
BACKGROUND In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35 S rDNA units (L-type). The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5 S genes in several species from family Asteraceae known to contain linked 35 S-5 S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays. RESULTS We found that homogenization of L-type units went to completion in most (4/6) but not all species. Two species contained major L-type and minor S-type units (termed L(s)-type). The linked genes dominate 5 S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5'-RGSWTGGGTG-3') is proposed. The 5 S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35 S-5 S arrays with nucleolar periphery indicating that transcription of 5 S genes may occur in this territory. CONCLUSIONS We show that the unusual linked arrangement of 5 S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5 S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs.
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MESH Headings
- Animals
- Asteraceae/chemistry
- Asteraceae/genetics
- Asteraceae/metabolism
- Base Sequence
- Consensus Sequence
- DNA Methylation
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Epigenesis, Genetic
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Regulatory Sequences, Nucleic Acid
- Response Elements
- Sequence Alignment
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Affiliation(s)
- Sònia Garcia
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s. n., Barcelona, Catalonia, 08028, Spain
| | - Lucie Crhák Khaitová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, CZ-6125, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, CZ-6125, Czech Republic
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Wicke S, Costa A, Muñoz J, Quandt D. Restless 5S: the re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants. Mol Phylogenet Evol 2011; 61:321-32. [PMID: 21757016 DOI: 10.1016/j.ympev.2011.06.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 06/23/2011] [Accepted: 06/27/2011] [Indexed: 01/16/2023]
Abstract
Among eukaryotes two types of nuclear ribosomal DNA (nrDNA) organization have been observed. Either all components, i.e. the small ribosomal subunit, 5.8S, large ribosomal subunit, and 5S occur tandemly arranged or the 5S rDNA forms a separate cluster of its own. Generalizations based on data derived from just a few model organisms have led to a superimposition of structural and evolutionary traits to the entire plant kingdom asserting that plants generally possess separate arrays. This study reveals that plant nrDNA organization into separate arrays is not a distinctive feature, but rather assignable almost solely to seed plants. We show that early diverging land plants and presumably streptophyte algae share a co-localization of all rRNA genes within one repeat unit. This raises the possibility that the state of rDNA gene co-localization had occurred in their common ancestor. Separate rDNA arrays were identified for all basal seed plants and water ferns, implying at least two independent 5S rDNA transposition events during land plant evolution. Screening for 5S derived Cassandra transposable elements which might have played a role during the transposition events, indicated that this retrotransposon is absent in early diverging vascular plants including early fern lineages. Thus, Cassandra can be rejected as a primary mechanism for 5S rDNA transposition in water ferns. However, the evolution of Cassandra and other eukaryotic 5S derived elements might have been a side effect of the 5S rDNA cluster formation. Structural analysis of the intergenic spacers of the ribosomal clusters revealed that transposition events partially affect spacer regions and suggests a slightly different transcription regulation of 5S rDNA in early land plants. 5S rDNA upstream regulatory elements are highly divergent or absent from the LSU-5S spacers of most early divergent land plant lineages. Several putative scenarios and mechanisms involved in the concerted relocation of hundreds of 5S rRNA gene copies are discussed.
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Affiliation(s)
- Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstr. 1, D-48149 Muenster, Germany.
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Garcia S, Lim KY, Chester M, Garnatje T, Pellicer J, Vallès J, Leitch AR, Kovarík A. Linkage of 35S and 5S rRNA genes in Artemisia (family Asteraceae): first evidence from angiosperms. Chromosoma 2008; 118:85-97. [PMID: 18779974 DOI: 10.1007/s00412-008-0179-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 07/22/2008] [Accepted: 08/20/2008] [Indexed: 10/24/2022]
Abstract
Typically in plants, the 5S and 35S ribosomal DNA (rDNA) encoding two major ribosomal RNA species occur at separate loci. However, in some algae, bryophytes and ferns, they are at the same locus (linked arranged). Southern blot hybridisation, polymerase chain reactions (PCR), fluorescent in situ hybridisation, cloning and sequencing were used to reveal 5S and 35S rDNA genomic organisation in Artemisia. We observed thousands of rDNA units at two-three loci containing 5S rDNA in an inverted orientation within the inter-genic spacer (IGS) of 35S rDNA. The sequenced clones of 26-18S IGS from Artemisia absinthium appeared to contain a conserved 5S gene insertion proximal to the 26S gene terminus (5S rDNA-1) and a second less conserved 5S insertion (5S rDNA-2) further downstream. Whilst the 5S rDNA-1 showed all the structural features of a functional gene, the 5S-rDNA-2 had a deletion in the internal promoter and probably represents a pseudogene. The linked arrangement probably evolved before the divergence of Artemisia from the rest of Asteraceae (>10 Myrs). This arrangement may have involved retrotransposons and once formed spread via mechanisms of concerted evolution. Heterogeneity in unit structure may reflect ongoing homogenisation of variant unit types without fixation for any particular variant.
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Affiliation(s)
- Sònia Garcia
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Catalonia, Spain
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Fulnecek J, Kovarik A. Low abundant spacer 5S rRNA transcripts are frequently polyadenylated in Nicotiana. Mol Genet Genomics 2007; 278:565-73. [PMID: 17671796 DOI: 10.1007/s00438-007-0273-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 06/22/2007] [Accepted: 06/27/2007] [Indexed: 10/23/2022]
Abstract
In plants, 5S rRNA genes (5S rDNA) encoding 120-nt structural RNA molecules of ribosomes are organized in tandem arrays comprising thousands of units. Failure to correctly terminate transcription would generate longer inaccurately processed transcripts interfering with ribosome biogenesis. Hence multiple termination signals occur immediately after the 5S rRNA coding sequence. To obtain information about the efficiency of termination of 5S rDNA transcription in plants we analyzed 5S rRNA pools in three Nicotiana species, N. sylvestris, N. tomentosiformis and N. tabacum. In addition to highly abundant 120-nt 5S rRNA transcripts, we also detected RNA species composed of a genic region and variable lengths of intergenic sequences. These genic-intergenic RNA molecules occur at a frequency severalfold lower than the mature 120-nt transcripts, and are posttranscriptionally modified by polyadenylation at their 3' end in contrast to 120-nt transcripts. An absence of 5S small RNAs (smRNA) argue against a dominant role for the smRNA biosynthesis pathway in the degradation of aberrant 5S rRNA in Nicotiana. This work is the first description of polyadenylated 5S rRNA species in higher eukaryotes originating from a read-through transcription into the intergenic spacer. We propose that polyadenylation may function in a "quality control" pathway ensuring that only correctly processed molecules enter the ribosome biogenesis.
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Affiliation(s)
- Jaroslav Fulnecek
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i, Kralovopolska 135, 612 65, Brno, Czech Republic.
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Hansen H, Martinsen L, Bakke TA, Bachmann L. The incongruence of nuclear and mitochondrial DNA variation supports conspecificity of the monogenean parasites Gyrodactylus salaris and G. thymalli. Parasitology 2006; 133:639-50. [PMID: 16863602 DOI: 10.1017/s0031182006000655] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 05/13/2006] [Accepted: 05/13/2006] [Indexed: 11/07/2022]
Abstract
The monogenean Gyrodactylus salaris Malmberg, 1957 is an economically important parasite on Atlantic salmon whereas the morphologically very similar G. thymalli Zitnan, 1960 on grayling is considered harmless. Even molecular markers cannot unambiguously discriminate both species. The nuclear internal transcribed spacer (ITS) sequences are identical in both species, and although mitochondrial cytochrome oxidase I (COI) sequences show substantial variation, no support for monophyly of either species is found. Analysis of nucleotide sequences of the intergenic spacer (IGS) have, however, been interpreted as support for 2 species. Here, IGS and COI sequences from 81 G. salaris and G. thymalli specimens of 39 populations across the species' distribution range were determined. Mitochondrial diversity was not reflected in the nuclear marker. Since various 23 bp IGS repeat types usually differ by just one nucleotide and sequences primarily differ in the number and order of repeat types, alignments may be biased and arbitrary, impeding meaningful phylogenetic analyses. The hypothesis that parasites on rainbow trout represent hybrids of both species is rejected. The presence or absence of particular repeat types is not considered informative. We interpret the IGS data as support for G. salaris and G. thymalli being a single species.
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Affiliation(s)
- H Hansen
- Natural History Museum, Department for Zoology, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway.
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Hemleben V, Volkov RA, Zentgraf U, Medina FJ. Molecular Cell Biology: Organization and Molecular Evolution of rDNA, Nucleolar Dominance, and Nucleolus Structure. PROGRESS IN BOTANY 2004. [DOI: 10.1007/978-3-642-18819-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Volkov RA, Komarova NY, Panchuk II, Hemleben V. Molecular evolution of rDNA external transcribed spacer and phylogeny of sect. Petota (genus Solanum). Mol Phylogenet Evol 2003; 29:187-202. [PMID: 13678676 DOI: 10.1016/s1055-7903(03)00092-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 5(') external transcribed spacer (ETS) region of ribosomal DNA of 30 species of Solanum sect. Petota and the European Solanum dulcamara were compared. Two structural elements can be distinguished in the ETS: (i). a variable region (VR), demonstrating significant structural rearrangements and (ii). a conservative region (CR), evolving mainly by base substitutions. In VR, a conservative element (CE) with similarity to the ETS of distantly related Nicotiana is present. The ancestral organization of ETS (variant A) was found for non-tuber-bearing species of ser. Etuberosa, tuber-bearing wild potatoes of Central American ser. Bulbocastana, Pinnatisecta, and Polyadenia and S. dulcamara. Duplication of CE took place in the ETS of species from ser. Commersoniana and Circaeifolia (variant B). South American diploids and Mexican polyploids from superser. Rotata also possess two CE, and additionally two duplications around CE1 are present in VR (variant C). Three major lineages could be distinguished: non-tuber-bearing species of ser. Etuberosa, tuber-bearing Central American diploids and all South American species radiated from a common ancestor at early stages of evolution, indicating a South American origin of the tuber-bearing species. Later, Central and South American diploids evolved further as independent lineages. South American species form a monophyletic group composed of series with both stellata and rotata flower morphology. Solanum commersonii represents a sister taxon for all rotata species, whereas ser. Circaeifolia diverged earlier. Two main groups, C1 and C2, may be distinguished for species possessing ETS variant C. C1 contains ser. Megistacroloba, Conicibaccata, Maglia, and Acaulia, whereas all diploids of ser. Tuberosa are combined into C2. A closer relationship of Solanum chacoense (ser. Yungasensa) to the C2 group was found. The origin of polyploid species Solanum maglia, Solanum acaule, Solanum tuberosum, Solanum iopetalum, and Solanum demissum is discussed.
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Affiliation(s)
- Roman A Volkov
- Department of General Genetics, Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
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Pikaard CS. Transcription and tyranny in the nucleolus: the organization, activation, dominance and repression of ribosomal RNA genes. THE ARABIDOPSIS BOOK 2002; 1:e0083. [PMID: 22303219 PMCID: PMC3243331 DOI: 10.1199/tab.0083] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Craig S Pikaard
- Biology Department, Washington University, Campus box 1137, 1 Brookings Drive, St. Louis, Missouri, 63130, USA ; FAX: 314-935-4432;
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Markos S, Baldwin BG. Structure, molecular evolution, and phylogenetic utility of the 5(') region of the external transcribed spacer of 18S-26S rDNA in Lessingia (Compositae, Astereae). Mol Phylogenet Evol 2002; 23:214-28. [PMID: 12069552 DOI: 10.1016/s1055-7903(02)00004-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The 18S-26S nuclear rDNA external transcribed spacer (ETS) has recently gained attention as a region that is valuable in phylogenetic analyses of angiosperms primarily because it can supplement nucleotide variation from the widely used and generally shorter internal transcribed spacers (ITS-1 and ITS-2) and thereby improve phylogenetic resolution and clade support in rDNA trees. Subrepeated ETS sequences (often occurring in the 5(') region) can, however, create a challenge for systematists interested in using ETS sequence data for phylogeny reconstruction. We sequenced the 5(')ETS for members of Lessingia (Compositae, Astereae) and close relatives (26 taxa total) to characterize the subrepeat variation across a group of closely related plant lineages and to gain improved understanding of the structure, molecular evolution, and phylogenetic utility of the region. The 5(')ETS region of Lessingia and relatives varied in length from approximately 245 to 1009 bp due to the presence of a variable number of subrepeats (one to eight). We assessed homology of the subrepeats using phylogenetic analysis and concluded that only two of the subrepeats and a portion of a third ( approximately 282 bp in total) were orthologous across Lessingia and could be aligned with confidence and included in further analyses. When the partial 5(')ETS data were combined with 3(')ETS and ITS data in phylogenetic analyses, no additional resolution of relationships among taxa was obtained beyond that found from analysis of 3(')ETS + ITS sequences. Inferred patterns of concerted evolution indicate that homogenization is occurring at a faster rate in the 3(')ETS and ITS regions than in the 5(')ETS region. Additionally, homogenization appears to be acting within but not among subrepeats of the same rDNA array. We conclude that challenges in assessing subrepeat orthology across taxa greatly limit the utility of the 5(')ETS region for phylogenetic analyses among species of Lessingia.
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MESH Headings
- Asteraceae/classification
- Asteraceae/genetics
- Base Sequence
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/genetics
- Evolution, Molecular
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Staci Markos
- Jepson Herbarium and Department of Integrative Biology, University of California, Berkeley, CA 94720-2465, USA.
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17
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Fernández M, Polanco C, Ruiz ML, Pérez de la Vega M. A comparative study of the structure of the rDNA intergenic spacer of Lens culinaris Medik., and other legume species. Genome 2000; 43:597-603. [PMID: 10984170 DOI: 10.1139/g00-022] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As part of a project on lentil molecular genetics, the sequence of the 18S-25S ribosomal RNA gene intergenic spacer (IGS) of Lens culinaris Medik. was determined. DNA was cloned after polymerase chain reaction (PCR) amplification. The spacer of 2939 bp was composed of nonrepetitive sequences and four tandem arrays of repeated sequences, named A to D. C and D arrays were formed by the repetition of very short consensus sequences. Similarity was found between lentil and other legume species, in particular those of the Vicieae tribe. A transcription initiation site, putative sites of termination and processing, and promoter-enhancer sequences were detected by computer-aided searches. These sites resemble motifs conserved in the IGS sequences of other plant species. The conservation of motifs in the otherwise highly variable plant IGS sequences points to the relevance of these motifs as functional sequences.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- Consensus Sequence
- DNA Methylation
- DNA, Intergenic
- DNA, Ribosomal/genetics
- Fabaceae/genetics
- Genes, Plant
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plants, Medicinal
- Polymerase Chain Reaction
- Promoter Regions, Genetic
- RNA/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- Transcription, Genetic
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Affiliation(s)
- M Fernández
- Departamento de Genética, Facultad de Biología, Universidad de León, Spain
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18
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Jobst J, King K, Hemleben V. Molecular evolution of the internal transcribed spacers (ITS1 and ITS2) and phylogenetic relationships among species of the family Cucurbitaceae. Mol Phylogenet Evol 1998; 9:204-19. [PMID: 9562980 DOI: 10.1006/mpev.1997.0465] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phylogenetic relationships of different members of the family Cucurbitaceae were estimated from sequences of the internal transcribed spacer (ITS1 and ITS2) regions of the nuclear ribosomal RNA genes. Twenty-six species of different genera belonging to different tribes and several subtribes were analyzed. The whole ITS regions were amplified by PCR technique and cloned, and three to five different clones of each species were sequenced; for some species PCR products were sequenced directly. ITS1 and ITS2 regions are slightly variable in length, with each length appearing genus-specific. A substitution rate of 3.62 x 10(-9) substitutions per site per year was calculated assuming 40 MYA separation time. Phylogenetic relationships inferred from ITS sequences of some species is in agreement with morphological data, but deviations to the taxonomic classification were also observed. A polyphyletic origin of the New World species must be considered. In the genus Cucurbita different "types" of ITS sequences within one species exist, possibly due to the high frequency of introgression during domestication or due to polyploidization events; in contrast, low intraspecific variability was detectable in the genus Cucumis, indicating different stages of speciation.
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Affiliation(s)
- J Jobst
- Department of Genetics, University of Tuebingen, Germany
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19
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Doelling JH, Pikaard CS. Species-specificity of rRNA gene transcription in plants manifested as a switch in RNA polymerase specificity. Nucleic Acids Res 1996; 24:4725-32. [PMID: 8972859 PMCID: PMC146310 DOI: 10.1093/nar/24.23.4725] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Rapid evolution of ribosomal RNA (rRNA) gene promoters often prevents their recognition in a foreign species. Unlike animal systems, we show that foreign plant rRNA gene promoters are recognized in an alien species, but tend to program transcription by a different polymerase. In plants, RNA polymerase I transcripts initiate at a TATATA element (+1 is underlined) important for promoter strength and start-site selection. However, transcripts initiate from +32 following transfection of a tomato promoter into Arabidopsis. The rRNA gene promoter of a more closely related species, Brassica oleracea, programs both +1 and +29 transcription. A point mutation at +2 improving the identity between the Brassica and Arabidopsis promoters increases +1 transcription, indicating a role for the initiator element in species-specificity. Brassica +29 transcripts can be translated to express a luciferase reporter gene, implicating RNA polymerase II. TATA mutations that disrupt TATA-binding protein (TBP) interactions inhibit +29 transcription and luciferase expression. Co-expressed TBP proteins bearing compensatory mutations restore +29 transcription and luciferase activity, suggesting a direct TBP-TATA interaction. Importantly, +1 transcription is unaffected by the TATA mutations, suggesting that in the context of pol I recognition, the TATA-containing initiator element serves a function other than TBP binding.
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Affiliation(s)
- J H Doelling
- Biology Department, Washington University, St Louis, MO 63130, USA
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20
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Bhatia S, Singh Negi M, Lakshmikumaran M. Structural analysis of the rDNA intergenic spacer of Brassica nigra: evolutionary divergence of the spacers of the three diploid Brassica species. J Mol Evol 1996; 43:460-8. [PMID: 8875860 DOI: 10.1007/bf02337518] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
EcoRI restriction of the B. nigra rDNA recombinants, isolated from a lambda genomic library, showed that the 3.9-kb fragment corresponded to the Intergenic Spacer (IGS), which was sequenced and found to be 3,928 bp in size. Sequence and dot-matrix analyses showed that the organization of the B. nigra rDNA IGS was typical of most rDNA spacers, consisting of a central repetitive region and flanking unique sequences on either side. The repetitive region was composed of two repeat families-RF 'A' and RF 'B.' The B. nigra RF 'A' consisted of a tandem array of three full-length copies of a 106-bp sequence element. RF 'B' was composed of 66 tandemly repeated elements. Each 'B' element was only 21-bp in size and this is the smallest repeat unit identified in plant rDNA to date. The putative transcription initiation site (TIS) was identified as nucleotide position 3,110. Based on the sequence analysis it was suggested that the present organization of the repeat families was generated by successive cycles of deletions and amplifications and was being maintained by homogenization processes such as gene conversion and crossing-over.A detailed comparison of the rDNA IGS sequences of the three diploid Brassica species-namely, B. nigra, B. campestris, and B. oleracea-was carried out. First, comparisons revealed that B. campestris and B. oleracea were close to each other as the repeat families in both showed high sequence homology between each other. Second, the repeat elements in both the species were organized in an interspersed manner. Third, a 52-bp sequence, present just downstream of the repeats in B. campestris, was found to be identical to the B. oleracea repeats, thereby suggesting a common progenitor. On the other hand, in B. nigra no interspersion pattern of organization of repeats was observed. Further, the B. nigra RF 'A' was identified as distinct from the repeat families of B. campestris and B. oleracea. Based on this analysis, it was suggested that during speciation B. campestris and B. oleracea evolved in one lineage whereas B. nigra diverged into a separate lineage. The comparative analysis of the IGS helped in identifying not only conserved ancestral sequence motifs of possible functional significance such as promoters and enhancers, but also sequences which showed variation between the three diploid species and were therefore identified as species-specific sequences.
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Affiliation(s)
- S Bhatia
- Biotechnology Division, Tata Energy Research Institute, Darbari Seth Block, Habitat Place, Lodhi Road, New Delhi-110 003, India
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21
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Haberer G, Fischer TC, Torres-Ruiz RA. Mapping of the nucleolus organizer region on chromosome 4 in Arabidopsis thaliana. MOLECULAR & GENERAL GENETICS : MGG 1996; 250:123-8. [PMID: 8569682 DOI: 10.1007/bf02191832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In Arabidopsis thaliana the ribosomal RNA genes (rRNA genes or rDNA) are clustered in tandemly repeated blocks in two nucleolus organizer regions (NORs). Cytogenetic analysis has shown that the NORs are localized on chromosome 2 (NOR 2) and 4 (NOR 4). Recently the map position of NOR 2 was determined using a RFLP which was larger than 100 kb. In the course of a fingerprint analysis of different Arabidopsis ecotypes we have detected four rDNA polymorphisms between the ecotypes Landsberg (La) and Niederzenz (Nd). Mapping of these polymorphisms using established segregating F2 populations reveals that all polymorphisms detected are dominant. Three of them map to the locus on the second chromosome that has been shown to harbour the NOR 2. The fourth polymorphism can be unambiguously assigned to the upper arm of the fourth chromosome. This is the first polymorphism found which originates in the second rDNA cluster of Arabidopsis thaliana. It enables localization of NOR 4 and thus completes the mapping of rDNA genes in the NORs of Arabidopsis.
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Affiliation(s)
- G Haberer
- Lehrstuhl für Genetik, Ludwig-Maximilians-Universität München, Germany
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22
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Da Rocha PS, Bertrand H. Structure and comparative analysis of the rDNA intergenic spacer of Brassica rapa. Implications for the function and evolution of the Cruciferae spacer. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 229:550-7. [PMID: 7744079 DOI: 10.1111/j.1432-1033.1995.tb20497.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The sequence of the intergenic spacer (IGS) of the Brassica rapa rDNA was determined and compared with those of other Cruciferae species. In the 3012-bp IGS, two segments of mostly unique sequence flank a 1.5-kb region consisting of two tandem arrays of repeats. A putative transcription initiation site (TIS) was identified by sequence comparison, 395 bp downstream from the repeat region. The intercalating segment displays unusual sequence patterns, and modelling of its topology predicts intrinsically bent DNA, with two elements of bending centered at positions -118 and -288 relative to the TIS. Comparative analysis of spacers from Cruciferae, revealed a common organization and high sequence similarity in their 5' and, particularly, 3' regions, whereas the repeat region upstream of TIS diverges rapidly. The conservation of structural elements, including the bent DNA upstream from the TIS, is discussed in light of their possible involvement in the IGS functions and structure of spacers in common ancestors. Examination of the Cruciferae spacers shows that, in addition to unequal crossover and gene conversion, insertional mutagenesis and replication slippage are molecular mechanisms significantly contributing to their evolution.
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Affiliation(s)
- P S Da Rocha
- Department of Microbiology, University of Guelph, Ontario, Canada
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23
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Torres-Ruiz RA, Hemleben V. Pattern and degree of methylation in ribosomal RNA genes of Cucurbita pepo L. PLANT MOLECULAR BIOLOGY 1994; 26:1167-1179. [PMID: 7811974 DOI: 10.1007/bf00040697] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Methylation with respect to its degree and distribution throughout the 18S, 5.8S and 25S rRNA gene clusters (rDNA) and within single rDNA repeats in seedlings of the higher plant Cucurbita pepo L. (zucchini) was investigated. In this plant, which is characterized by several thousand repeats, at least 70% are completely or nearly completely methylated in CpGs and to a lower degree in CpNpGs. Detailed methylation analysis revealed that a fraction of about 3-4% of all repeats is hypomethylated near the transcription initiation site (TIS) which may indicate the fraction of active repeats in C. pepo. However, a different fraction (3-4% of all repeats) which is not methylated in all sites tested (including those at the TIS) is present in C. pepo and may thus represent active but differentially methylated rDNA. The results are discussed in context of recent models on methylation and gene activity.
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Affiliation(s)
- R A Torres-Ruiz
- Lehrstuhl für Genetik, Ludwig Maximilians Universität München, FRG
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24
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Polanco C, Pérez de la Vega M. The structure of the rDNA intergenic spacer of Avena sativa L.: a comparative study. PLANT MOLECULAR BIOLOGY 1994; 25:751-756. [PMID: 8061326 DOI: 10.1007/bf00029613] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The sequence of the 18S-25S ribosomal RNA gene intergenic spacer (IGS) of Avena sativa was determined. DNA was cloned after polymerase chain reaction amplification of the IGS. The spacer of 3980 bp is composed of non-repeated sequences and five tandem arrays of repeated sequences, named A to E. Homology between oats IGS and other grass species was found. Tandem arrays D and E seem to be originated by duplication from single-copy sequences in related species. A transcription initiation site and putative sites of termination, processing and methylation were detected by computer-aided search. These sites resemble motifs conserved in the IGS of plant species.
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Affiliation(s)
- C Polanco
- Departamento de Genética, Facultad de Biología, Universidad de León, Spain
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25
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Fukuoka H, Kageyama Y, Yamamoto K, Takeda G. Rapid conversion of rDNA intergenic spacer of diploid mutants of rice derived from gamma-ray irradiated tetraploids. MOLECULAR & GENERAL GENETICS : MGG 1994; 243:166-72. [PMID: 7909914 DOI: 10.1007/bf00280313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The organization of tandemly repeated sequences of ribosomal DNA (rDNA) in rice mutants derived from gamma-irradiated tetraploids was analyzed. Southern hybridization analysis of nuclear DNA revealed that most of the intergenic spacers (IGSs) in mutant rDNA are replaced concertedly by new molecular species. The new IGSs are produced by the amplification of a subrepeat of about 250 bp. Results obtained from sequence analyses indicate that various intermediate molecular species of the subrepeat were formed during structuring of the IGS region and that many rearrangements occurred between them. These findings demonstrate the effectiveness of recurrent irradiation of tetraploids for inducing artificial genome rearrangement, and also indicate the extreme plasticity and variability of genome structure in plants.
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Affiliation(s)
- H Fukuoka
- Laboratory of Plant Breeding, Faculty of Agriculture, University of Tokyo, Japan
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26
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Hemleben V, Zentgraf U. Structural organization and regulation of transcription by RNA polymerase I of plant nuclear ribosomal RNA genes. Results Probl Cell Differ 1994; 20:3-24. [PMID: 8036320 DOI: 10.1007/978-3-540-48037-2_1] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- V Hemleben
- Department of Genetics, Biological Institute, University of Tübingen, FRG
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27
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Zentgraf U, Hemleben V. Nuclear proteins interact with RNA polymerase I promoter and repeated elements of the 5' external transcribed spacer of the rDNA of cucumber in a single-stranded stage. PLANT MOLECULAR BIOLOGY 1993; 22:1153-1156. [PMID: 8400131 DOI: 10.1007/bf00028984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Directly repeated elements have been characterized downstream of the transcription initiation site (TIS) in the 5' external transcribed spacer (5' ETS) of the rRNA genes of cucumber (Cucumis sativus). In order to show that these repeated elements are also involved in transcriptional regulation processes of RNA polymerase I while being single-stranded during transcription, DNA-protein binding assays were performed with synthetic oligonucleotides prepared from the promoter region as well as from the repeated elements. The single-stranded DNA of the upstream binding element (from -164 to -105), the core promoter (from -41 to +16) and a loop-forming sequence (LRE) of the repeated elements interact with the same nuclear proteins whereas another region of the repeated elements (XRE) cooperates with a different nuclear protein. Remarkably, both complementary strands show identical protein binding.
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Affiliation(s)
- U Zentgraf
- Lehrstuhl für Allgemeine Genetik, Universität Tübingen, Germany
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28
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Doelling JH, Gaudino RJ, Pikaard CS. Functional analysis of Arabidopsis thaliana rRNA gene and spacer promoters in vivo and by transient expression. Proc Natl Acad Sci U S A 1993; 90:7528-32. [PMID: 8356050 PMCID: PMC47175 DOI: 10.1073/pnas.90.16.7528] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In eukaryotes, RNA polymerase I transcription is controlled by DNA elements located within the spacers that separate the tandemly arranged rRNA genes. Unlike rRNA coding sequences, the intergenic spacers evolve rapidly and have little sequence similarity even among closely related species. Nonetheless, the arrangement of functional elements, such as spacer promoters and enhancers, is thought to be highly conserved. Here, we identify spacer promoters in the plant Arabidopsis thaliana, thereby demonstrating their existence in both the plant and animal kingdoms. We also use an Arabidopsis transient expression system to perform transcriptional analysis of the ribosomal gene promoter. Spacer promoters share sequence similarity with the gene promoter from -91 to +22 relative to the transcription start site, +1. Deletion analysis shows that sequences required for RNA polymerase I transcription reside within these boundaries. Spacer sequences upstream of the gene promoter have only a small positive effect on transcription in transfected protoplasts but can increase transcription from a Xenopus ribosomal gene promoter in injected frog oocytes. This trans-kingdom enhancer effect further suggests that the functional elements within eukaryotic ribosomal genes are highly conserved.
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Affiliation(s)
- J H Doelling
- Biology Department, Washington University, St. Louis, MO 63130
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29
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Cordesse F, Cooke R, Tremousaygue D, Grellet F, Delseny M. Fine structure and evolution of the rDNA intergenic spacer in rice and other cereals. J Mol Evol 1993; 36:369-79. [PMID: 8315657 DOI: 10.1007/bf00182184] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The intergenic spacer of a rice ribosomal RNA gene repeating unit has been completely sequenced. The spacer contains three imperfect, direct repeated regions of 264-253 bp, followed by a related but more highly divergent region. Detailed analysis of the sequence allows the presentation of an evolutionary scenario in which the 264-253-bp repeats are derived from an ancestral 150-bp sequence by deletion and amplification. Comparison of the rice sequence with those of maize, wheat, and rye shows that, despite considerable divergence from the ancestral sequence, several regions have been highly conserved, suggesting that they may play an important role in the structure and/or expression of the ribosomal genes.
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Affiliation(s)
- F Cordesse
- Laboratoire de Physiologie et Biologie Moléculaire Végétales, URA 565 du Centre National de la Recherche Scientifique, Université de Perpignan, France
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30
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King K, Torres RA, Zentgraf U, Hemleben V. Molecular evolution of the intergenic spacer in the nuclear ribosomal RNA genes of cucurbitaceae. J Mol Evol 1993; 36:144-52. [PMID: 8433383 DOI: 10.1007/bf00166250] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The intergenic spacer (IGS) of a 10-kbp repeat (clone pRZ7D) of the nuclear 18S, 5.8S, and 25S ribosomal RNA genes of Cucurbita pepo (zucchini) was sequenced and compared to the IGS sequences of two other Cucurbitaceae, Curcurbita maxima (squash), and Cucumis sativus (cucumber). The nucleotide sequence and the structural organization of the IGS of C. pepo and C. maxima are rather similar (between 75 and 100% sequence similarity depending on the region compared). The IGS are mainly composed of three different repeated elements interspersed into unique sequences: GC-rich clusters, a 422-bp AT-rich element including the transcription initiation site (TIS) for RNA polymerase I, and 260-bp repeats in the 5' external transcribed spacer (D repeats). The TIS is duplicated in the 10-kbp repeat class of C. pepo, as it is also described for the 11.5-kbp rDNA repeat of C. maxima. The IGS of Cucumis sativus is also composed of different repeated elements; however, obvious sequence identity to the Cucurbita species only occurs around the TIS and the preceding AT-rich region. GC-rich clusters with different primary sequences are present in the IGS of all three plants. Remarkably, the repeated elements in the 5'ETS accumulate TpG and TpNpG motifs, whereas CpG and CpNpG motifs less frequently occur. This accumulation might be caused by the transition of methylated cytosines (in mCpG or mCpNpG motifs) into thymidine via deamination in a previously GC-rich ancestor. The following singular region exhibits 50% G + C in C. pepo, 53% G+C in C. maxima, and 63% G + C in C. sativus.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- K King
- Institut für Mikrobiologie und Genetik, Universität München, Federal Republic of Germany
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31
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Borisjuk N, Hemleben V. Nucleotide sequence of the potato rDNA intergenic spacer. PLANT MOLECULAR BIOLOGY 1993; 21:381-4. [PMID: 8425062 DOI: 10.1007/bf00019953] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The large intergenic spacer (IGS) of potato rDNA was sequenced and compared to the IGS sequence of tomato. Both spacers exhibit similar length and architecture. Absence of repeated elements down-stream of the putative transcription initiation site (TIS) in potato is compensated by the larger number of subrepeats upstream of the TIS. Especially high level of similarity (86% and 86.5%, respectively) is found in the AT-rich domain containing the TIS and the region approx. 800 bp upstream of the 18S rRNA gene.
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Affiliation(s)
- N Borisjuk
- Biologisches Institut der Universität Tübingen, Lehrstuhl für Allgemeine Genetik, Germany
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32
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Zentgraf U, Hemleben V. Complex formation of nuclear proteins with the RNA polymerase I promoter and repeated elements in the external transcribed spacer of Cucumis sativus ribosomal DNA. Nucleic Acids Res 1992; 20:3685-91. [PMID: 1641334 PMCID: PMC334019 DOI: 10.1093/nar/20.14.3685] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Complex repetitive structures are located downstream of the transcription initiation site in the intergenic spacer (IGS) of the rRNA genes in Cucumis sativus (cucumber). In order to show that these repetitive elements of the 5'external transcribed spacer (ETS) are probably involved in transcriptional regulation as protein binding sites DNA-protein binding assays were carried out. The same proteins that recognize two binding sites in the promoter region analysed (upstream binding element between -164 and -105, and core promoter between -41 and +16) show binding affinity to the complex structures of the 5'external transcribed spacer. These proteins also seem to interact with the single strands of the respective DNA regions suggesting an effect on transcriptional regulation while the DNA is transcribed and, therefore, is single-stranded. Three proteins were isolated by affinity column chromatography; these proteins turned out to be much smaller (16, 22, and 24 kDa, respectively) than promoter and enhancer binding proteins in animal systems. Additionally, a 70-kDa protein could be characterized cooperating with a small segment of the repeated elements but not with the promoter.
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Affiliation(s)
- U Zentgraf
- Lehrstuhl für Allgemeine Genetik, Biologisches Institut, Tübingen, Germany
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33
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Baldridge GD, Fallon AM. Primary structure of the ribosomal DNA intergenic spacer from the mosquito, Aedes albopictus. DNA Cell Biol 1992; 11:51-9. [PMID: 1739434 DOI: 10.1089/dna.1992.11.51] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have determined the primary structure of a 4.7-kb portion of the ribosomal DNA intergenic spacer from cultured cells of the mosquito, Aedes albopictus. Immediately upstream from the 18S rRNA gene was a 753-bp sequence containing two regions similar to known RNA polymerase I promoters, each preceded by potential transcription termination signals. Upstream from this putative promoter region was a 3.15-kb tandem array of 17 direct repeats with a consensus sequence length of 201 bp. The 201-bp repeats contained imperfect antisense duplications of 11-bp core domain regions in the putative RNA polymerase I promoters, and sequences of possible significance in recombination. Farthest upstream of the 18S rRNA gene was an 803-bp region containing two copies each of 34-, 48-, and 64-bp elements separated by apparently unique sequence. This first detailed structural analysis of a ribosomal DNA intergenic spacer from a member of the lower Diptera has revealed features similar to those described for the higher Diptera as well as conserved motifs presumably critical to rRNA transcription.
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Affiliation(s)
- G D Baldridge
- Department of Entomology, University of Minnesota, St. Paul 55108
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