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Kim M, Lee SH, Jeon J. A Nucleolar Protein, MoRRP8 Is Required for Development and Pathogenicity in the Rice Blast Fungus. MYCOBIOLOGY 2023; 51:273-280. [PMID: 37929010 PMCID: PMC10621250 DOI: 10.1080/12298093.2023.2257996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023]
Abstract
The nucleolus is the largest, membrane-less organelle within the nucleus of eukaryotic cell that plays a critical role in rRNA transcription and assembly of ribosomes. Recently, the nucleolus has been shown to be implicated in an array of processes including the formation of signal recognition particles and response to cellular stress. Such diverse functions of nucleolus are mediated by nucleolar proteins. In this study, we characterized a gene coding a putative protein containing a nucleolar localization sequence (NoLS) in the rice blast fungus, Magnaporthe oryzae. Phylogenetic and domain analysis suggested that the protein is orthologous to Rrp8 in Saccharomyces cerevisiae. MoRRP8-GFP (translational fusion of MoRRP8 with green fluorescence protein) co-localizes with a nucleolar marker protein, MoNOP1 fused to red fluorescence protein (RFP), indicating that MoRRP8 is a nucleolar protein. Deletion of the MoRRP8 gene caused a reduction in vegetative growth and impinged largely on asexual sporulation. Although the asexual spores of ΔMorrp8 were morphologically indistinguishable from those of wild-type, they showed delay in germination and reduction in appressorium formation. Our pathogenicity assay revealed that the MoRRP8 is required for full virulence and growth within host plants. Taken together, these results suggest that nucleolar processes mediated by MoRRP8 is pivotal for fungal development and pathogenesis.
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Affiliation(s)
- Minji Kim
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
| | - Song Hee Lee
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
| | - Junhyun Jeon
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
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2
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Luo Y, Fefelova E, Ninova M, Chen YCA, Aravin AA. Repression of interrupted and intact rDNA by the SUMO pathway in Drosophila melanogaster. eLife 2020; 9:e52416. [PMID: 33164748 PMCID: PMC7676866 DOI: 10.7554/elife.52416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/06/2020] [Indexed: 11/17/2022] Open
Abstract
Ribosomal RNAs (rRNAs) are essential components of the ribosome and are among the most abundant macromolecules in the cell. To ensure high rRNA level, eukaryotic genomes contain dozens to hundreds of rDNA genes, however, only a fraction of the rRNA genes seems to be active, while others are transcriptionally silent. We found that individual rDNA genes have high level of cell-to-cell heterogeneity in their expression in Drosophila melanogaster. Insertion of heterologous sequences into rDNA leads to repression associated with reduced expression in individual cells and decreased number of cells expressing rDNA with insertions. We found that SUMO (Small Ubiquitin-like Modifier) and SUMO ligase Ubc9 are required for efficient repression of interrupted rDNA units and variable expression of intact rDNA. Disruption of the SUMO pathway abolishes discrimination of interrupted and intact rDNAs and removes cell-to-cell heterogeneity leading to uniformly high expression of individual rDNA in single cells. Our results suggest that the SUMO pathway is responsible for both repression of interrupted units and control of intact rDNA expression.
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Affiliation(s)
- Yicheng Luo
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Elena Fefelova
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Institute of Molecular Genetics, Russian Academy of SciencesMoscowRussian Federation
| | - Maria Ninova
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Yung-Chia Ariel Chen
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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3
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Conter CC, Mota CA, Dos Santos BA, de Souza Braga L, de Souza Terron M, Navasconi TR, Fernandes ACBS, Demarchi IG, de Castro KRR, Aristides SMA, Lonardoni MVC, Teixeira JJV, Silveira TGV. PCR primers designed for new world Leishmania: A systematic review. Exp Parasitol 2019; 207:107773. [PMID: 31605671 DOI: 10.1016/j.exppara.2019.107773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Accepted: 10/07/2019] [Indexed: 01/03/2023]
Abstract
Studies of the primers that were designed to detect New World Leishmania were systematically reviewed to report the characteristics of each target, detection limit, specificity of the primers designed and diagnostic sensibility. The papers identified in the databases PubMed and Web of Science involved 50 studies. Minicircle is the most applied target in molecular research for diagnosis, due to its high sensitivity in detecting Leishmania in different clinical samples, a characteristic that can be partially attributed to the higher number of copies of the minicircle per cell. The other molecular targets shown in this review were less sensitive to diagnostic use because of the lower number of copies of the target gene per cell, but more specific for identification of the subgenus and/or species. The choice of the best target is an important step towards the result of the research. The target allows the design of primers that are specific to the genus, subgenus or a particular species and also imparts sensitivity to the method for diagnosis. The findings of this systematic review provide the advantages and disadvantages of the main molecular targets and primers designed for New World Leishmania, offering information so that the researcher can choose the PCR system best suited to their research need. This is a timely and extremely thorough review of the primers designed for New World Leishmania.
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Affiliation(s)
- Carolina Cella Conter
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | - Camila Alves Mota
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Laís de Souza Braga
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Taísa Rocha Navasconi
- Graduate Program in Health Sciences, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Izabel Galhardo Demarchi
- Department of Clinical Analyses and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
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Kurose D, Furuya N, Saeki T, Tsuchiya K, Tsushima S, Seier MK. Species-Specific Detection of Mycosphaerella polygoni-cuspidati as a Biological Control Agent for Fallopia japonica by PCR Assay. Mol Biotechnol 2016; 58:626-633. [PMID: 27389682 PMCID: PMC5429361 DOI: 10.1007/s12033-016-9962-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The ascomycete fungus Mycosphaerella polygoni-cuspidati has been undergoing evaluation as a potential classical biological control agent for the invasive weed Fallopia japonica (Japanese knotweed), which has become troublesome in Europe and North America. In advance of the potential release of a biocontrol agent into a new environment, it is crucial to develop an effective monitoring system to enable the evaluation of agent establishment and dispersal within the target host population, as well as any potential attacks on non-target species. Therefore, a primer pair was designed for direct, rapid, and specific detection of the Japanese knotweed pathogen M. polygoni-cuspidati based on the sequences of the internal transcribed spacer regions including the 5.8S rDNA. A PCR product of approximately 298 bp was obtained only when the DNA extracted from mycelial fragments of M. polygoni-cuspidati was used. The lower limit of detection of the PCR method was 100 fg of genomic DNA. Using the specific primer pair, M. polygoni-cuspidati could be detected from both naturally and artificially infected Japanese knotweed plants. No amplification was observed for other Mycosphaerella spp. or fungal endophytes isolated from F. japonica. The designed primer pair is thus effective for the specific detection of M. polygoni-cuspidati in planta.
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Affiliation(s)
- Daisuke Kurose
- CABI Europe-UK, Bakeham Lane, Egham, Surrey, TW20 9TY, UK.
| | - Naruto Furuya
- Laboratory of Plant Pathology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Tetsuya Saeki
- Laboratory of Plant Pathology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Kenichi Tsuchiya
- Laboratory of Plant Pathology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Seiya Tsushima
- Plant Pathology Laboratory, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan
| | - Marion K Seier
- CABI Europe-UK, Bakeham Lane, Egham, Surrey, TW20 9TY, UK
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5
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Torres-Machorro AL, Hernández R, Cevallos AM, López-Villaseñor I. Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? FEMS Microbiol Rev 2010; 34:59-86. [DOI: 10.1111/j.1574-6976.2009.00196.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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6
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Ryu S, Do Y, Fitch DHA, Kim W, Mishra B. Dropout Alignment Allows Homology Recognition and Evolutionary Analysis of rDNA Intergenic Spacers. J Mol Evol 2008; 66:368-83. [DOI: 10.1007/s00239-008-9090-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 12/14/2007] [Accepted: 02/21/2008] [Indexed: 11/28/2022]
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7
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Waterhouse RN, Boulter D, Gatehouse JA. An organ-specific hypomethylation of cotyledon genomic rDNA in Pisum sativum
L. FEBS Lett 2001. [DOI: 10.1016/0014-5793(86)81115-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Greenwood SJ, Schnare MN, Cook JR, Gray MW. Analysis of intergenic spacer transcripts suggests 'read-around' transcription of the extrachromosomal circular rDNA in Euglena gracilis. Nucleic Acids Res 2001; 29:2191-8. [PMID: 11353089 PMCID: PMC55454 DOI: 10.1093/nar/29.10.2191] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2001] [Accepted: 03/21/2001] [Indexed: 11/14/2022] Open
Abstract
We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3'-end of the large subunit ribosomal RNA (rRNA) gene from the 5'-end of the small subunit (SSU) rRNA gene in the circular, extrachromosomal ribosomal DNA (rDNA) of Euglena gracilis. The IGS contains a 277 nt stretch of sequence that is related to a sequence found in ITS 1, an internal transcribed spacer between the SSU and 5.8S rRNA genes. Primer extension analysis of IGS transcripts identified three abundant reverse transcriptase stops that may be analogous to the transcription initiation site (TIS) and two processing sites (A' and A0) that are found in this region in other eukaryotes. Features that could influence processing at these sites include an imperfect palindrome near site A0 and a sequence near site A' that could potentially base pair with U3 small nucleolar RNA. Our identification of the TIS (verified by mung bean nuclease analysis) is considered tentative because we also detected low-abundance transcripts upstream of this site throughout the entire IGS. This result suggests the possibility of 'read-around' transcription, i.e. transcription that proceeds multiple times around the rDNA circle without termination.
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MESH Headings
- Animals
- Base Pairing
- Base Sequence
- Conserved Sequence/genetics
- DNA, Circular/genetics
- DNA, Intergenic/genetics
- DNA, Ribosomal/genetics
- Euglena/genetics
- Molecular Sequence Data
- Nuclease Protection Assays
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/metabolism
- Regulatory Sequences, Nucleic Acid/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Single-Strand Specific DNA and RNA Endonucleases/metabolism
- Transcription, Genetic/genetics
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Affiliation(s)
- S J Greenwood
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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9
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Robinett CC, O'Connor A, Dunaway M. The repeat organizer, a specialized insulator element within the intergenic spacer of the Xenopus rRNA genes. Mol Cell Biol 1997; 17:2866-75. [PMID: 9111359 PMCID: PMC232139 DOI: 10.1128/mcb.17.5.2866] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have identified a novel activity for the region of the intergenic spacer of the Xenopus laevis rRNA genes that contains the 35- and 100-bp repeats. We devised a new assay for this region by constructing DNA plasmids containing a tandem repeat of rRNA reporter genes that were separated by the 35- and 100-bp repeat region and a rRNA gene enhancer. When the 35- and 100-bp repeat region is present in its normal position and orientation at the 3' end of the rRNA reporter genes, the enhancer activates the adjacent downstream promoter but not the upstream rRNA promoter on the same plasmid. Because this element can restrict the range of an enhancer's activity in the context of tandem genes, we have named it the repeat organizer (RO). The ability to restrict enhancer action is a feature of insulator elements, but unlike previously described insulator elements the RO does not block enhancer action in a simple enhancer-blocking assay. Instead, the activity of the RO requires that it be in its normal position and orientation with respect to the other sequence elements of the rRNA genes. The enhancer-binding transcription factor xUBF also binds to the repetitive sequences of the RO in vitro, but these sequences do not activate transcription in vivo. We propose that the RO is a specialized insulator element that organizes the tandem array of rRNA genes into single-gene expression units by promoting activation of a promoter by its proximal enhancers.
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Affiliation(s)
- C C Robinett
- Department of Molecular and Cell Biology, University of California, Berkeley 94720-3202, USA
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10
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Yip CW, Liew CW, Nga BH. Ribosomal RNA genes ofEndomyces fibuliger: isolation, sequencing and the use of the 26S rRNA gene in integrative transformation ofSaccharomyces cerevisiae for efficient expression of the α-amylase gene ofEndomyces fibuliger. World J Microbiol Biotechnol 1997. [DOI: 10.1007/bf02770815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Sehgal D, Mittal V, Ramachandran S, Dhar SK, Bhattacharya A, Bhattacharya S. Nucleotide sequence organisation and analysis of the nuclear ribosomal DNA circle of the protozoan parasite Entamoeba histolytica. Mol Biochem Parasitol 1994; 67:205-14. [PMID: 7870125 DOI: 10.1016/0166-6851(94)00129-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have sequenced the extrachromsomal ribosomal DNA (rDNA) circle of the human protozoan parasite Entamoeba histolytica HM-1:IMSS and present here the complete sequence organisation of the 24.5-kb molecule. Each circle contains two 5.9-kb rDNA transcription units organised as inverted repeats. The regions downstream (3543 bp) and upstream (9216 bp) of the rDNAs contain various families of short tandem repeats. Some of the upstream repeats share extensive sequence homology with the downstream repeats. In addition to the rDNAs themselves, the rDNA circle appears to code for only one other transcript which is 0.7 kb in size as seen in Northern blots. From DNA sequence analysis, no open reading frame could be assigned to the transcript. Extrachromosomal rDNA circles also exist in other E. histolytica strains. Restriction enzyme maps of rDNA circles were constructed from E. histolytica strains 200:NIH, HK-9 and Rahman; and Entamoeba moshkovskii strain Laredo. Striking differences were observed in the organisation of some of them, e.g. the HK-9, Rahman and Laredo circles contained only one rDNA unit and lacked the 0.7-kb transcript sequence. The short repeat sequences upstream and downstream of rDNAs were present in HK-9 and Rahman but absent in Laredo. Circles with one rDNA unit may be derived from those with two units by homologous recombination at direct repeat sequences located upstream and downstream of the two rDNAs.
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Affiliation(s)
- D Sehgal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Indiana
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12
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13
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Baldridge GD, Dalton MW, Fallon AM. Is higher-order structure conserved in eukaryotic ribosomal DNA intergenic spacers? J Mol Evol 1992; 35:514-23. [PMID: 1474605 DOI: 10.1007/bf00160212] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Computer-based structural analysis of the ribosomal DNA intergenic spacer (IGS) from the mosquito Aedes albopictus revealed a potential to form strong and extensive secondary structures throughout a 4.7-kilobase (kb) region. The predicted stability of secondary structures was particularly high within a 3.15-kb region containing 17 tandem 201 base-pair subrepeats. Similarly strong secondary structure potential was also found when IGS subrepeats were analyzed from 17 phylogenetically diverse eukaryotes, including vertebrates, invertebrates, and plants. Conservation of higher-order structure potential in the IGS region of ribosomal DNA may reflect evolutionary and functional constraints on chromatin organization, transcriptional regulation of the ribosomal RNA genes, and/or transcript processing and stability.
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Affiliation(s)
- G D Baldridge
- Department of Entomology, University of Minnesota, St. Paul 55108
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14
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Ferrari S, Manfredini R, Grande A, Torelli G, Torelli U. Proliferation, differentiation arrest, and survival in leukemic blast cells. Ann N Y Acad Sci 1992; 663:202-14. [PMID: 1482054 DOI: 10.1111/j.1749-6632.1992.tb38664.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- S Ferrari
- Experimental Hematology Center, University of Modena, Italy
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15
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Xie W, O'Mahony DJ, Smith SD, Lowe D, Rothblum LI. Analysis of the rat ribosomal DNA promoter: characterization of linker-scanning mutants and of the binding of UBF. Nucleic Acids Res 1992; 20:1587-92. [PMID: 1579451 PMCID: PMC312242 DOI: 10.1093/nar/20.7.1587] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
To investigate the mechanism of transcription of the rat ribosomal DNA (rDNA) promoter, a series of 23 linker-scanning mutants were constructed and assayed in transfected CHO cells and with cell-free extracts. With minor variation, the results of the in vitro and in vivo assays paralleled one another. For example, these assays demonstrated that the mutagenesis of bases from -133 to -124, and those from -106 to -101 of the rDNA promoter significantly inhibited transcription both in vivo and in vitro. Both of these sites lie within the upstream promoter element (UPE) of the rDNA promoter. Several constructs, in particular one that mutated the bases between -49 and -45, were better promoters in vivo than the wild-type promoter. DNAse footprinting experiments with purified UBF, an RNA polymerase I transcription factor, demonstrated the importance of the bases between -106 and -101 for the binding of that factor, providing a positive correlation between the transcription experiments and the binding of UBF to the rDNA promoter.
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Affiliation(s)
- W Xie
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, PA 17822-2618
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16
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Bhattacharya S, Bhattacharya A, Diamond LS. Entamoeba histolytica extrachromosomal circular ribosomal DNA: analysis of clonal variation in a hypervariable region. Exp Parasitol 1992; 74:200-4. [PMID: 1346767 DOI: 10.1016/0014-4894(92)90047-e] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ribosomal RNA genes of the protozoan parasite Entamoeba histolytica are highly repeated and display restriction fragment length polymorphism. Using a set of four DNA probes spanning the coding region and part of the flanking region of the E. histolytica ribosomal RNA genes, an analysis of the DNA bands generated by EcoRI digestion of Entamoeba DNA is presented. This analysis included five strains of E. histolytica, four strains of E. moshkovskii, and one strain each of E. invadens and E. terrapinae. No common bands were observed between E. histolytica and the other Entamoeba. Within E. histolytica, two bands were conserved in all strains while the others were polymorphic. Detailed analysis of DNA from independently isolated clones of the strain HM-1:IMSS of E. histolytica showed two bands to be highly polymorphic. Of these, the 4.4-kb band of clone 6 was further analyzed. Polymorphism in this band could even be demonstrated in cells of the same clone. Restriction enzyme analysis of this DNA band from two clones of HM-1:IMSS showed that the polymorphism may be due to variable numbers of DraI repeat units present in this DNA stretch.
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Affiliation(s)
- S Bhattacharya
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
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17
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Liang S, Alksne L, Warner JR, Lacroute F. rna12+, a gene of Saccharomyces cerevisiae involved in pre-rRNA maturation. Characterization of a temperature-sensitive mutant, cloning and sequencing of the gene. MOLECULAR & GENERAL GENETICS : MGG 1992; 232:304-12. [PMID: 1557037 DOI: 10.1007/bf00280010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
RNA12-1 is a dominant temperature-sensitive (Ts) yeast mutant which has previously been reported to exhibit a defect in RNA accumulation at 37 degrees C. We further characterized this mutant through analyses of rRNA transcription rates and maturation. The results show that pre-rRNA is normally synthesized but that subsequent maturation is severely affected by a temperature upshift: the nascent rRNAs are under-methylated and little mature rRNA can be observed at 37 degrees C. Likewise, the accumulation of some mRNAs for ribosomal proteins is also prevented at 37 degrees C. The RNA12-1 mutation is recessive at 32 degrees C, which made it possible to clone the wild-type rna12+ gene by complementation of the Ts phenotype with plasmids from a multicopy yeast genomic library. The predicted gene product is a protein of 96,630 Da with no significant sequence similarity to any known proteins. Gene disruption is not lethal at either the permissive or the restrictive temperature. The gene is located on chromosome XIII, downstream of the ADH2 gene and 10 cM from the ADE4 gene. Furthermore, the mutant allele RNA12-1 was cloned and sequenced. A point mutation found in this allele leads to dominant thermosensitivity at 37 degrees C when the mutant gene is introduced into a wild-type strain. Taken together, these data suggest that the rna12+ gene product plays a dispensable role in early maturation of pre-rRNA but that its mutant gene product can interfere with the normal function of other proteins required for pre-rRNA maturation.
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Affiliation(s)
- S Liang
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
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18
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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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19
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Ghosh B, Datta U, Roy Choudhury S, Mandal RK. Size class homogeneity of repeat lengths and evolutionary divergence of ribosomal RNA genes in fishes as studied by restriction fragment length analysis. J Genet 1991. [DOI: 10.1007/bf02927867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Kitada K, Oka S, Kimura S, Shimada K, Serikawa T, Yamada J, Tsunoo H, Egawa K, Nakamura Y. Detection of Pneumocystis carinii sequences by polymerase chain reaction: animal models and clinical application to noninvasive specimens. J Clin Microbiol 1991; 29:1985-90. [PMID: 1774325 PMCID: PMC270246 DOI: 10.1128/jcm.29.9.1985-1990.1991] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Pneumocystis carinii is a eukaryotic microbe which causes fatal pneumonia in patients with AIDS. Oligonucleotide primers were used to amplify the 5S rDNA sequence of P. carinii by the polymerase chain reaction (PCR) in various clinical and animal samples. Of 35 independent lung specimens tested, PCR detected the P. carinii sequence in all 23 cases which were known to be P. carinii infected, i.e., 15 from mice, 1 from rat, 3 from human autopsy, and 4 from biopsy of AIDS patients by needle aspiration. The results were consistent with clinical and microscopic diagnosis. The detection was highly sensitive and specific. Direct sequencing of these amplified DNAs revealed homogeneity of 5S rDNA sequences of independent isolates from mice, rats, and humans. Preliminary trials manifested efficacy of the PCR method to detect P. carinii sequences in induced sputum or blood from AIDS patients, the latter case suggesting that P. carinii might enter peripheral blood via phagocytosis or direct intrusion. Development of less-invasive or noninvasive PCR diagnostic techniques to detect P. carinii infection would greatly facilitate therapeutic and prophylactic management of P. carinii pneumonia.
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MESH Headings
- Acquired Immunodeficiency Syndrome/complications
- Animals
- Base Sequence
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- Disease Models, Animal
- Evaluation Studies as Topic
- Humans
- Mice
- Mice, Nude
- Molecular Sequence Data
- Opportunistic Infections/complications
- Opportunistic Infections/diagnosis
- Opportunistic Infections/microbiology
- Pneumocystis/genetics
- Pneumocystis/isolation & purification
- Pneumonia, Pneumocystis/complications
- Pneumonia, Pneumocystis/diagnosis
- Pneumonia, Pneumocystis/microbiology
- Polymerase Chain Reaction/methods
- Polymerase Chain Reaction/statistics & numerical data
- RNA, Fungal/genetics
- RNA, Fungal/isolation & purification
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/isolation & purification
- Sensitivity and Specificity
- Sequence Homology, Nucleic Acid
- Species Specificity
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Affiliation(s)
- K Kitada
- Department of Tumor Biology, University of Tokyo, Japan
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21
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O'Mahony DJ, Rothblum LI. Identification of two forms of the RNA polymerase I transcription factor UBF. Proc Natl Acad Sci U S A 1991; 88:3180-4. [PMID: 2014238 PMCID: PMC51409 DOI: 10.1073/pnas.88.8.3180] [Citation(s) in RCA: 96] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The structure of the rat homologue of the RNA polymerase I transcription factor UBF was investigated. The sequence of the protein was deduced from the sequence of overlapping cDNAs isolated from a cDNA library and from clones of the products generated by the polymerase chain reaction from random-primed, first-strand cDNA. The sequences of these clones indicated that there were two mRNAs for UBF and that the encoded proteins were similar but not identical. One form of rat UBF was essentially identical to human UBF. The second class of UBF mRNA contained an in-frame "deletion" in the coding region that results in the deletion of 37 amino acids from the predicted protein sequence. This deletion reduces the predicted molecular size of the encoded form of UBF by approximately 4400 from 89.4 kDa to 85 kDa and significantly alters the structure of one of the four HMG-1 homology regions (HMG box-2) in that form of UBF. Evidence for the existence of two mRNAs in rat cells was confirmed by a probe protection assay, and we provide evidence that other vertebrate cells contain these same two forms of UBF mRNA. These results are consistent with the observation that UBF purified from four different vertebrates migrates as two bands upon SDS/PAGE. It has been hypothesized that the HMG motifs are the DNA-binding domains of UBF. Altering one of these "boxes," as in the second form of UBF, may alter the functional characteristics of the transcription factor. Thus, the existence of different forms of UBF may have important ramifications for transcription by RNA polymerase I.
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Affiliation(s)
- D J O'Mahony
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, PA 17822
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22
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Sequence organization and RNA structural motifs directing the mouse primary rRNA-processing event. Mol Cell Biol 1991. [PMID: 1986240 DOI: 10.1128/mcb.11.1.458] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first processing step in the maturation of mouse precursor rRNA involves cleavage at nucleotide ca. +650, at the 5' border of a 200-nucleotide region that is conserved across mammals and contains the sequences that direct the processing. To identify the relevant sequence elements, we used rRNAs with small internal mutations and short pre-rRNA substrates. Much of the region can be mutated without appreciable effect, but nucleotides +655 to +666 appear to be absolutely required and short segments surrounding +750 and +810 markedly stimulate processing. The minimal processing signal corresponds to rRNA nucleotides +645 to +672. Formation of a ribonucleoprotein complex of retarded electrophoretic mobility is evidently necessary but not sufficient for processing. Computer-assisted analysis suggested a phylogenetic- and mutant-supported secondary structure in which the minimal processing signal forms a stem with the +655 region in the loop, and there is a separate branched duplex containing the downstream stimulatory sequences. Use of antisense RNA, in trans and in cis, to sequester the +655 region in a duplex supported the hypothesis that this critical region was needed in a single-stranded conformation for processing and for specific complex formation.
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23
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Molecular Analysis of the Nucleolus Organizer Region in Maize. ACTA ACUST UNITED AC 1991. [DOI: 10.1016/b978-0-444-88259-2.50031-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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24
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Sequence organization and RNA structural motifs directing the mouse primary rRNA-processing event. Mol Cell Biol 1991; 11:458-67. [PMID: 1986240 PMCID: PMC359650 DOI: 10.1128/mcb.11.1.458-467.1991] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first processing step in the maturation of mouse precursor rRNA involves cleavage at nucleotide ca. +650, at the 5' border of a 200-nucleotide region that is conserved across mammals and contains the sequences that direct the processing. To identify the relevant sequence elements, we used rRNAs with small internal mutations and short pre-rRNA substrates. Much of the region can be mutated without appreciable effect, but nucleotides +655 to +666 appear to be absolutely required and short segments surrounding +750 and +810 markedly stimulate processing. The minimal processing signal corresponds to rRNA nucleotides +645 to +672. Formation of a ribonucleoprotein complex of retarded electrophoretic mobility is evidently necessary but not sufficient for processing. Computer-assisted analysis suggested a phylogenetic- and mutant-supported secondary structure in which the minimal processing signal forms a stem with the +655 region in the loop, and there is a separate branched duplex containing the downstream stimulatory sequences. Use of antisense RNA, in trans and in cis, to sequester the +655 region in a duplex supported the hypothesis that this critical region was needed in a single-stranded conformation for processing and for specific complex formation.
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25
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Heinonen TY, Schnare MN, Gray MW. Sequence heterogeneity in the duplicate large subunit ribosomal RNA genes of Tetrahymena pyriformis mitochondrial DNA. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)45710-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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Mahajan PB, Thompson EA. Hormonal regulation of transcription of rDNA. Purification and characterization of the hormone-regulated transcription factor IC. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)46212-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Zentgraf U, Ganal M, Hemleben V. Length heterogeneity of the rRNA precursor in cucumber (Cucumis sativus). PLANT MOLECULAR BIOLOGY 1990; 15:465-474. [PMID: 2103464 DOI: 10.1007/bf00019163] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The length homogeneous part of the intergenic spacer (IGS) of the 18S-25S ribosomal RNA genes of cucumber (Cucumis sativus) was characterized by sequencing 2389 bp preceding the 18S rRNA coding region of a 12.5 kbp repeat type. This part of the IGS is composed of repeated elements and shows a very complex structural organization. Most obvious is a 119 bp element which is repeated seven times. A single transcription initiation site (TIS) was detected by a 'T4 polymerase stop' experiment upstream of these repetitions giving rise to a 2013 bp 5' external transcribed spacer (ETS) for cucumber. Nuclease mapping showed several transcription termination sites (TTS): the first one is located 350 bp downstream of the 25S rRNA coding region, the others are found within the duplications of this region accounting for the length heterogeneity of cucumber rDNA. Therefore, the TTS is repeated two or three times in the IGS depending on the length of the respective repeat classes and the rRNA precursor is heterogeneous in length varying from approx. 8000 to 11000 nts.
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Affiliation(s)
- U Zentgraf
- Biologisches Institut der Universität Tübingen, FRG
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28
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Abstract
The protein components that direct and activate accurate transcription by rat RNA polymerase I were studied in extracts of Novikoff hepatoma ascites cells. A minimum of at least two components, besides RNA polymerase I, that are necessary for efficient utilization of templates were identified. The first factor, rat SL-1, is required for species-specific recognition of the rat RNA polymerase I promoter and may be sufficient to direct transcription by pure RNA polymerase I. Rat SL-1 directed the transcription of templates deleted to -31, the 5' boundary of the core promoter element (+1 being the transcription initiation site). The second factor, rUBF, increased the efficiency of template utilization. Transcription of deletion mutants indicated that the 5' boundary of the domain required for rUBF lay between -137 and -127. Experiments using block substitution mutants confirmed and extended these observations. Transcription experiments using those mutants demonstrated that two regions within the upstream promoter element were required for optimal levels of transcription in vitro. The first region was centered on nucleotides -129 and -124. The 5' boundary of the second domain mapped to between nucleotides -106 and -101. DNase footprint experiments using highly purified rUBF indicated that rUBF bound between -130 and -50. However, mutation of nucleotides -129 and -124 did not affect the rUBF footprint. These results indicate that basal levels of transcription by RNA polymerase I may require only SL-1 and the core promoter element. However, higher transcription levels are mediated by additional interactions of rUBF, and possibly SL-1, bound to distal promoter elements.
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29
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Smith SD, Oriahi E, Lowe D, Yang-Yen HF, O'Mahony D, Rose K, Chen K, Rothblum LI. Characterization of factors that direct transcription of rat ribosomal DNA. Mol Cell Biol 1990; 10:3105-16. [PMID: 2342470 PMCID: PMC360675 DOI: 10.1128/mcb.10.6.3105-3116.1990] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The protein components that direct and activate accurate transcription by rat RNA polymerase I were studied in extracts of Novikoff hepatoma ascites cells. A minimum of at least two components, besides RNA polymerase I, that are necessary for efficient utilization of templates were identified. The first factor, rat SL-1, is required for species-specific recognition of the rat RNA polymerase I promoter and may be sufficient to direct transcription by pure RNA polymerase I. Rat SL-1 directed the transcription of templates deleted to -31, the 5' boundary of the core promoter element (+1 being the transcription initiation site). The second factor, rUBF, increased the efficiency of template utilization. Transcription of deletion mutants indicated that the 5' boundary of the domain required for rUBF lay between -137 and -127. Experiments using block substitution mutants confirmed and extended these observations. Transcription experiments using those mutants demonstrated that two regions within the upstream promoter element were required for optimal levels of transcription in vitro. The first region was centered on nucleotides -129 and -124. The 5' boundary of the second domain mapped to between nucleotides -106 and -101. DNase footprint experiments using highly purified rUBF indicated that rUBF bound between -130 and -50. However, mutation of nucleotides -129 and -124 did not affect the rUBF footprint. These results indicate that basal levels of transcription by RNA polymerase I may require only SL-1 and the core promoter element. However, higher transcription levels are mediated by additional interactions of rUBF, and possibly SL-1, bound to distal promoter elements.
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Affiliation(s)
- S D Smith
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas
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30
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Smith SD, Oriahi E, Yang-Yen HF, Xie WQ, Chen C, Rothblum LI. Interaction of RNA polymerase I transcription factors with a promoter in the nontranscribed spacer of rat ribosomal DNA. Nucleic Acids Res 1990; 18:1677-85. [PMID: 2336355 PMCID: PMC330583 DOI: 10.1093/nar/18.7.1677] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The spacer promoter of the rat rDNA repeat consists of two functional domains: a core (proximal) element that is sufficient for transcription in vitro, and an upstream (distal) promoter element that increases the efficiency of transcription. Two of the transcription factors that interact with the 45S promoter also interact with the spacer promoter. Rat SL-1, is required for transcription of the spacer promoter by heterologous extracts, e.g. human, and rat SF-1 is required for efficient transcription in vitro. Order-of-addition experiments demonstrated that the preinitiation complex formed by these factors on the spacer promoter is not as stable as the complex formed on the 45S promoter. DNase 1 footprinting experiments demonstrated binding sites for rat SL-1 and SF-1 on the distal element of the spacer promoter. The topology of the domains of the spacer promoter may explain both the reduced stability of the preinitiation complex formed on that promoter and the lower efficiency of transcription of that promoter when compared to the 45S promoter.
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Affiliation(s)
- S D Smith
- Weis Center for Research, Geisinger Clinic, Danville, PA 17822
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31
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Grondal EJ, Evers R, Cornelissen AW. Identification and sequence analysis of the ribosomal DNA promoter region of Crithidia fasciculata. Nucleic Acids Res 1990; 18:1333-8. [PMID: 2326181 PMCID: PMC330495 DOI: 10.1093/nar/18.6.1333] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have identified the promoter region of the large ribosomal DNA repeat unit of Crithidia fasciculata by northern blotting and nuclear run-on analyses. These data show that transcription starts approximately 1 kb upstream of the 18S rRNA gene. S1 protection experiments and sequence analysis of this area resulted in a precise localization of the start site. We have been unable to identify conserved sequence element(s) by a direct comparison of the crithidial RNA polymerase I promoter region and similar promoter regions of other eukaryotes; not even to the promoter region of the more closely related kinetoplastid species, Trypanosoma brucei. The absence of homology within the primary sequence of the promoter region, which is also found in other eukaryotes, might explain the observed species specificity of in vivo and in vitro rDNA transcription, since this resides in the interaction of initiation factor(s) and the core promoter domain.
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Affiliation(s)
- E J Grondal
- Max-Planck-Institut für Biologie, Molecular Parasitology Unit, Tübingen, FRG
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32
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Kass S, Tyc K, Steitz JA, Sollner-Webb B. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell 1990; 60:897-908. [PMID: 2156625 DOI: 10.1016/0092-8674(90)90338-f] [Citation(s) in RCA: 370] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The first cleavage in mammalian pre-rRNA maturation occurs near the 5' end within the 5' external transcribed spacer. Using mouse cell extracts, we show that this processing is abolished by micrococcal nuclease pretreatment. Autoantibodies that recognize the U3, U8, and U13 snRNPs (anti-fibrillarin) deplete processing activity from the extract and selectively immunoprecipitate both rRNA substrates and processing products from the reaction. Specific involvement of the U3 snRNP is demonstrated by native gel electrophoresis of the processing reaction followed by Northern blotting and by oligonucleotide-directed RNAase H abolition of processing activity. Our identification of U3 function is discussed with respect to the molecular basis of pre-rRNA recognition by the U3 snRNP, possible roles of U3 and other nucleolar snRNPs in rRNA processing, and the morphological organization of the nucleolus and the ribosomal transcription complex.
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Affiliation(s)
- S Kass
- Human Genetics Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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33
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Stroke IL, Weiner AM. The 5' end of U3 snRNA can be crosslinked in vivo to the external transcribed spacer of rat ribosomal RNA precursors. J Mol Biol 1989; 210:497-512. [PMID: 2614831 DOI: 10.1016/0022-2836(89)90126-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
From previous work it was known that U3 RNA is hydrogen bonded to nucleolar 28 S to 35 S RNA and can be covalently crosslinked to RNA of greater than 28 S by irradiation in vivo with long-wave ultraviolet light in the presence of 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT psoralen). Here we use a novel sandwich blot technique to identify these large nucleolar RNA species as rRNA precursors and to map the site(s) of crosslinking in vivo. The crosslink occurs between one or more residues near the 5' end of U3 RNA and a 380 nucleotide region of the rat rRNA external transcribed spacer (ETS1). We have sequenced this region of the rat ETS and we show that it includes an RNA-processing site analogous to those previously mapped to approximately 3.5 kb upstream from the 5' end of mouse and human 18 S rRNAs.
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Affiliation(s)
- I L Stroke
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510
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34
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van der Sande CA, Kulkens T, Kramer AB, de Wijs IJ, van Heerikhuizen H, Klootwijk J, Planta RJ. Termination of transcription by yeast RNA polymerase I. Nucleic Acids Res 1989; 17:9127-46. [PMID: 2685755 PMCID: PMC335119 DOI: 10.1093/nar/17.22.9127] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Analysis of the termination of transcription by yeast RNA polymerase I (Pol I) using in vitro run-on experiments in both isolated nuclei and permeabilized cells demonstrated that Pol I does not traverse the whole intergenic spacer separating consecutive 37S operons, but terminates transcription before reaching the 5S rRNA gene, that is within NTS 1. In order to discriminate between processing and termination at the 3'-end generating sites previously identified in vivo in NTS 1 (T1, T2 and T3), fragments containing these sites were inserted into the middle of the reporter DNA of an artificial rRNA minigene. RNA isolated from yeast cells transformed with these minigenes was analyzed for the presence of transcripts derived from sequences both up- and downstream of the insert by Northern blot hybridization, reverse transcription analysis and S1 nuclease mapping. In accordance with previously obtained results T1 (+15 to +50) was found to behave as a processing site. T2 (+210) however was concluded to be an efficient, genuine Pol I terminator. In addition to T2, two other terminators were identified in NTS 1: T3A (at +690) and T3B (at +950). Surprisingly, when the 3' terminal part of NTS 2 was tested for its capacity to generate 3'-ends, another terminator (Tp) was found to be present at a position 300 bp upstream of the transcription initiation site of the 37S-rRNA operon.
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Affiliation(s)
- C A van der Sande
- Biochemisch Laboratorium, Vrije Universiteit, Amsterdam, The Netherlands
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35
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Yoganathan T, Lin H, Buck GA. An electrophoretic karyotype and assignment of ribosomal genes to resolved chromosomes of Pneumocystis carinii. Mol Microbiol 1989; 3:1473-80. [PMID: 2615653 DOI: 10.1111/j.1365-2958.1989.tb00132.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pulsed-field gel electrophoresis was used to generate a molecular karyotype of chromosomes from the opportunistic AIDS pathogen, Pneumocystis carinii. P. carinii cysts and trophozoites were isolated from immunosuppressed rats, lysed in situ in agarose blocks, and subjected to orthogonal-field gel electrophoresis (OFAGE) and contour-clamped homogeneous-field gel electrophoresis (CHEF). OFAGE and CHEF gels resolved, respectively, 16 or 20 chromosome bands ranging in size from 0.32-1.5 megabase pairs. Summation of the estimated sizes of these chromosomes suggested a total genome complexity for P. carinii of 8-16 megabase pairs. Homologous probes for the genes encoding the 18S, 5.8S, and 5S ribosomal RNAs were hybridized to filter blots of the pulsed-field gels to map these genes to specific P. carinii chromosomes.
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Affiliation(s)
- T Yoganathan
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond 23298
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36
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Bhattacharya S, Bhattacharya A, Diamond LS, Soldo AT. Circular DNA of Entamoeba histolytica encodes ribosomal RNA. THE JOURNAL OF PROTOZOOLOGY 1989; 36:455-8. [PMID: 2553935 DOI: 10.1111/j.1550-7408.1989.tb01080.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The presence of repeated DNA sequences encoding RNA in Entamoeba histolytica has been reported. In the present study we demonstrate by agarose gel electrophoresis. DNase digestion and electron microscopic analysis that these genes are located on extrachromosomal circular DNA molecules with an approximate size of 26 kb. Detection of replication intermediates suggests the episomal nature of these molecules. Amplified, extrachromosomal rRNA genes appear to be a common feature among the lower eukaryotes, occurring more commonly as linear molecules and less commonly as circles. Entamoeba histolytica is 1 of the few organisms studied in which rRNA genes are located predominantly on extrachromosomal circles.
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MESH Headings
- Animals
- Blotting, Southern
- DNA Probes
- DNA Replication
- DNA, Circular/analysis
- DNA, Circular/genetics
- DNA, Circular/ultrastructure
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- DNA, Ribosomal/ultrastructure
- Deoxyribonuclease I/metabolism
- Electrophoresis, Agar Gel
- Entamoeba histolytica/genetics
- Microscopy, Electron
- Nucleic Acid Hybridization
- RNA, Ribosomal/genetics
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Affiliation(s)
- S Bhattacharya
- Laboratory of Parasitic Diseases, NIAID, Bethesda, Maryland 20892
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37
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Purification and characterization of a high-mobility-group-like DNA-binding protein that stimulates rRNA synthesis in vitro. Mol Cell Biol 1989. [PMID: 3211145 DOI: 10.1128/mcb.8.8.3406] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A 16,000-dalton, high-mobility-group-like (HMG-like) DNA-binding protein, referred to as p16, has been purified to homogeneity from Novikoff hepatoma ascites cells. p16 binds specifically to a portion of the 5' flanking region of the rat rRNA gene (-620 to -417), which is part of the upstream activator sequence identified previously (B. G. Cassidy, H.-F. Yang-Yen, and L. I. Rothblum, Mol. Cell. Biol. 6:2766-2773, 1986). p16 also binds to a segment of the external transcribed spacer (+352 to +545). In vitro reconstituted transcription experiments demonstrated that the addition of p16 stimulated rRNA synthesis up to ca. fourfold. The stimulation was dose dependent and saturable. The effect of p16 on ribosomal gene transcription was also dependent on the presence of either the upstream or the downstream DNA-binding site, or both. The amino acid composition of p16 is very similar to that of HMG-I, suggesting that p16 may be a member of the HMG-I family of proteins. In this case, our results suggest that HMG proteins may play an important role in the regulation of the rRNA gene expression.
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38
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White TC, Fase-Fowler F, van Luenen H, Calafat J, Borst P. The H circles of Leishmania tarentolae are a unique amplifiable system of oligomeric DNAs associated with drug resistance. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37486-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Developmental regulation of the methylation of the ribosomal DNA in the basidiomycete fungusSchizophyllum commune. Curr Genet 1988. [DOI: 10.1007/bf00569333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Grimaldi G, Di Nocera PP. Multiple repeated units in Drosophila melanogaster ribosomal DNA spacer stimulate rRNA precursor transcription. Proc Natl Acad Sci U S A 1988; 85:5502-6. [PMID: 2840664 PMCID: PMC281785 DOI: 10.1073/pnas.85.15.5502] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Drosophila melanogaster ribosomal DNA (rDNA) transcriptional units are separated by nontranscribed spacer (NTS) segments consisting of tandemly arranged repeats 95, 330, and 240 base pairs long. NTS sequences stimulate transcription from the rRNA precursor (pre-rRNA) promoter. Primer extension analysis of RNA from cells cotransfected with plasmids carrying NTS sequences of various lengths shows that the activity of the pre-rRNA promoter is directly correlated with the number of 240-base-pair repeats; NTS sequences upstream of these units also stimulate pre-rRNA transcription. The NTS effect might depend upon transcription from duplicated promoters present within the 240- and 330-base-pair repeats. The strength of the pre-RNA promoter correlates in each construct with the level of spacer transcription. The action of spacer sequences, although able to take place over a large distance, is not independent of orientation: stimulation of pre-rRNA transcription is abolished in plasmids carrying inverted NTS segments. Removal of a putative transcription termination site located upstream of the pre-rRNA promoter has no effect on pre-rRNA initiation nor does it substantially alter spacer enhancement.
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Affiliation(s)
- G Grimaldi
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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41
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Yang-Yen HF, Rothblum LI. Purification and characterization of a high-mobility-group-like DNA-binding protein that stimulates rRNA synthesis in vitro. Mol Cell Biol 1988; 8:3406-14. [PMID: 3211145 PMCID: PMC363577 DOI: 10.1128/mcb.8.8.3406-3414.1988] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A 16,000-dalton, high-mobility-group-like (HMG-like) DNA-binding protein, referred to as p16, has been purified to homogeneity from Novikoff hepatoma ascites cells. p16 binds specifically to a portion of the 5' flanking region of the rat rRNA gene (-620 to -417), which is part of the upstream activator sequence identified previously (B. G. Cassidy, H.-F. Yang-Yen, and L. I. Rothblum, Mol. Cell. Biol. 6:2766-2773, 1986). p16 also binds to a segment of the external transcribed spacer (+352 to +545). In vitro reconstituted transcription experiments demonstrated that the addition of p16 stimulated rRNA synthesis up to ca. fourfold. The stimulation was dose dependent and saturable. The effect of p16 on ribosomal gene transcription was also dependent on the presence of either the upstream or the downstream DNA-binding site, or both. The amino acid composition of p16 is very similar to that of HMG-I, suggesting that p16 may be a member of the HMG-I family of proteins. In this case, our results suggest that HMG proteins may play an important role in the regulation of the rRNA gene expression.
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Affiliation(s)
- H F Yang-Yen
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030
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42
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Ravel-Chapuis P. Nuclear rDNA in Euglena gracilis: paucity of chromosomal units and replication of extrachromosomal units. Nucleic Acids Res 1988; 16:4801-10. [PMID: 3133636 PMCID: PMC336697 DOI: 10.1093/nar/16.11.4801] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Copy number of chromosomal rDNA units was investigated in two Euglena gracilis wild-type strains. It was established by dot blot analysis that these strains possess about four integrated units per haploid genome. This is the first example of a photosynthetic cell with only a few chromosomal ribosomal genes. In addition to these units, Euglena has 800 to 4000 extrachromosomal rDNA units. Electron microscopy revealed that these free rDNA circles bear a replication origin, and intermediates of replication show a D-loop structure.
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Affiliation(s)
- P Ravel-Chapuis
- Université Lyon I, Laboratoire de Biologie Cellulaire, UA CNRS 92, Villeurbanne, France
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43
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Ganal M, Torres R, Hemleben V. Complex structure of the ribosomal DNA spacer of Cucumis sativus (cucumber). MOLECULAR & GENERAL GENETICS : MGG 1988; 212:548-54. [PMID: 3419423 DOI: 10.1007/bf00330863] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The nuclear 18 S, 5.8 S and 25 S ribosomal RNA genes (rDNA) of Cucumis sativus (cucumber) occur in at least four different repeat types of 10.2, 10.5, 11.5, and 12.5 kb in length. The intergenic spacer of these repeats has been cloned and characterized with respect to sequence organization. The spacer structure is very unusual compared to those of other eukaryotes. Duplicated regions of 197 bp and 311 bp containing part of the 3'end of the 25 S rRNA coding region and approximately 470 bp of 25 S rRNA flanking sequences occur in the intergenic spacer. The data from sequence analysis suggest that these duplications originate from recombination events in which DNA sequences of the original rDNA spacer were paired with sequences of the 25 S rRNA coding region. The duplicated 3'ends of the 25 S rRNA are separated from each other mostly by a tandemly repeated 30 bp element showing a high GC-content of 87.5%. In addition, another tandemly repeated sequence of 90 bp was found downstream of the 3'flanking sequences of the 25 S rRNA coding region. These results suggest that rRNA coding sequences can be involved in the generation of rDNA spacer sequences by unequal crossing over.
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Affiliation(s)
- M Ganal
- Institut für Biologie II, Universität Tübingen, Federal Republic of Germany
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44
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Barker RF, Harberd NP, Jarvis MG, Flavell RB. Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat. J Mol Biol 1988; 201:1-17. [PMID: 3418693 DOI: 10.1016/0022-2836(88)90434-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The complete nucleotide sequence of the intergenic region between the 25 S and 18 S wheat ribosomal RNA genes has been determined from a 4.6 kb EcoRI-BamHI fragment (1 kb = 10(3) bases or base-pairs) subcloned from the plasmid pTa71. Within this subclone the intergenic DNA is flanked by the 3' end of the 25 S and the 5' end of the 18 S ribosomal RNA sequences. Four repeat families are present within the intergenic region. The major repeat family A, consists of 12 direct repeat units of 135 or 136 base-pairs (bp) flanked by diverged truncated copies. Within each A repeat a subrepeat structure has been revealed. Family B, which is localized to the 5' side of the A repeats, contains three repeat units, one of 152 bp, the second of 150 bp and a truncated unit of 107 bp. Family C, which is localized in the transcribed rRNA precursor, consists of two direct repeat units of 172 and 174 bp and possesses some short subrepeat motifs. The C repeats may have evolved by and diverged from one another by the insertion of short transposable sequences. Family D consists of two direct repeat units of 30 bp located 5' to the start of transcription. Statistical analysis of repeat family A showed that there is a significant association between the similarity of any two repeat units and their distance apart in the array. The near identity of members of the A family is maintained presumably by processes such as unequal crossing over and gene conversion, but the members at each end of the array show more divergence. Sequence motifs in the A and C repeat families and in other regions including the 5' end of 18 S RNA are related, implying that much of the intergenic DNA may have evolved from a few short ancestral sequences. The B and D repeats or their equivalent are not found in a maize ribosomal DNA repeat unit. The DNA in the external transcribed spacer DNA 5' to the 18 S RNA sequence is longer in wheat than in maize. This is due principally to two duplications and insertion of a sequence with dyad symmetry in the wheat gene.
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Affiliation(s)
- R F Barker
- Department of Molecular Genetics, AFRC Institute of Plant Science Research (Cambridge Laboratory), Trumpington, U.K
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45
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Buckner B, Novotny CP, Ullrich RC. Organization of the ribosomal RNA genes of Schizophyllum commune. Curr Genet 1988; 13:417-24. [PMID: 2841031 DOI: 10.1007/bf00365663] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The 18, 5.8, 25 and 5S ribosomal RNA (rRNA) cistrons have been mapped on the ribosomal DNA (rDNA) unit repeat of Schizophyllum commune strain 4-40. These genes are spatially ordered in the sequence given. The presence of a large primary precursor rRNA which is processed to form the mature 18, 5.8 and 25S rRNAs has been demonstrated. We have mapped the site of transcriptional initiation for this rRNA primary precursor. The sequence surrounding this site has been determined and shown to be highly conserved, with considerable identity to those in Neurospora crassa and Dictyostelium discoideum. The direction of transcription of the rRNA genes has been determined. The 5S rRNA cistron is transcribed in the same direction as the other rRNAs, however it is not transcribed as a part of the large primary precursor. The previously identified rDNA strain-specific length polymorphisms (Specht et al. 1984) are shown to be located within the transcribed region of the rDNA unit repeat.
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Affiliation(s)
- B Buckner
- Department of Botany, University of Vermont, Burlington 05405
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46
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rRNA genes of Naegleria gruberi are carried exclusively on a 14-kilobase-pair plasmid. Mol Cell Biol 1987. [PMID: 2823115 DOI: 10.1128/mcb.7.9.3027] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An extrachromosomal DNA was discovered in Naegleria gruberi. The 3,000 to 5,000 copies per cell of this 14-kilobase-pair circular plasmid carry all the 18S, 28S, and 5.8S rRNA genes. The presence of the ribosomal DNA of an organism exclusively on a circular extrachromosomal element is without precedent, and Naegleria is only the third eucaryotic genus in which a nuclear plasmid DNA has been found.
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47
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Edlind TD, Chakraborty PR. Unusual ribosomal RNA of the intestinal parasite Giardia lamblia. Nucleic Acids Res 1987; 15:7889-901. [PMID: 3118329 PMCID: PMC306315 DOI: 10.1093/nar/15.19.7889] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The anaerobic protozoan Giardia lamblia is a common intestinal parasite in humans, but is poorly defined at molecular and phylogenetic levels. We report here a structural characterization of the ribosomal RNA (rRNA) and rRNA genes of G. lamblia. Gel electrophoresis under native or non-denaturing conditions identified two high molecular weight rRNA species corresponding to the 16-18S and 23-28S rRNAs. Surprisingly, both species (1300 and 2300 nucleotides long, respectively) were considerably shorter than their counterparts from other protozoa (typically 1800 and 3400 nucleotides), and from bacteria as well (typically 1540 and 2900 nucleotides long). Denaturing polyacrylamide gel electrophoresis identified a major low molecular RNA of 127 nucleotides and several minor species, but no molecules with the typical lengths of 5.8S (160 nucleotides) and 5S (120 nucleotides) rRNA. The G. lamblia 1300, 2300, and 127 nucleotide RNAs are encoded within a 5.6 kilobase pair tandemly repeated DNA, as shown by Southern blot analysis and DNA cloning. Thus, the rRNA operon of this eukaryotic organism can be no longer than a typical bacterial operon. Sequence analysis identified the 127 nucleotide RNA as homologous to 5.8S RNA, but comparisons to archaebacterial rRNA suggest that Giardia derived from an early branch in eukaryotic evolution.
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Affiliation(s)
- T D Edlind
- Department of Microbiology and Immunology, Medical College of Pennsylvania, Philadelphia 19129
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48
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Johnson AM, Murray PJ, Illana S, Baverstock PJ. Rapid nucleotide sequence analysis of the small subunit ribosomal RNA of Toxoplasma gondii: evolutionary implications for the Apicomplexa. Mol Biochem Parasitol 1987; 25:239-46. [PMID: 3320746 DOI: 10.1016/0166-6851(87)90087-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A method for obtaining a large proportion of the nucleotide sequence of the small subunit ribosomal RNA (srRNA) was applied to the obligate intracellular protozoon Toxoplasma gondii. The method uses reverse transcription of as little as 8 micrograms of total cellular RNA. This fast, efficient method has numerous advantages over traditional gene cloning methods when nucleotide sequences are required for evolutionary studies. A phylogenetic analysis of the srRNA sequence data showed that T. gondii is not especially closely related to any other organism for which srRNA sequences are available, including another member of the Apicomplexa.
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Affiliation(s)
- A M Johnson
- Unit of Clinical Microbiology, School of Medicine, Flinders University of South Australia, Bedford Park
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49
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Additional RNA polymerase I initiation site within the nontranscribed spacer region of the rat rRNA gene. Mol Cell Biol 1987. [PMID: 3614195 DOI: 10.1128/mcb.7.7.2388] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified and characterized an additional promoter within the nontranscribed spacer (NTS) of the rat ribosomal gene repeat that is capable of supporting initiation of transcription by RNA polymerase I in vitro. Within this promoter there is a sequence of 13 nucleotides which is 100% homologous to nucleotides -18 to -6 (+1 being the first nucleotide of 45S rRNA) of the major promoter of 45S pre-rRNA and is located between nucleotides -731 and -719. To identify the exact location of the upstream initiation site, the RNA synthesized in vitro from this new promoter was gel isolated and subjected to fingerprint analysis, Southern hybridization, and reverse transcriptase elongation. Based on these analyses, the in vitro-synthesized RNA initiates with an A at nucleotide -713. When compared individually, the upstream promoter was transcribed ninefold less efficiently than the major promoter. When templates which contain both promoters on the same piece of DNA were transcribed, the major promoter was at least 50-fold more efficient.
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50
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Clark CG, Cross GA. rRNA genes of Naegleria gruberi are carried exclusively on a 14-kilobase-pair plasmid. Mol Cell Biol 1987; 7:3027-31. [PMID: 2823115 PMCID: PMC367933 DOI: 10.1128/mcb.7.9.3027-3031.1987] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An extrachromosomal DNA was discovered in Naegleria gruberi. The 3,000 to 5,000 copies per cell of this 14-kilobase-pair circular plasmid carry all the 18S, 28S, and 5.8S rRNA genes. The presence of the ribosomal DNA of an organism exclusively on a circular extrachromosomal element is without precedent, and Naegleria is only the third eucaryotic genus in which a nuclear plasmid DNA has been found.
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Affiliation(s)
- C G Clark
- Rockefeller University, New York, New York 10021-6399
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