501
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Bryan GT, Daniels MJ, Osbourn AE. Comparison of fungi within the Gaeumannomyces-Phialophora complex by analysis of ribosomal DNA sequences. Appl Environ Microbiol 1995; 61:681-9. [PMID: 7574606 PMCID: PMC167329 DOI: 10.1128/aem.61.2.681-689.1995] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Four ascomycete species of the genus Gaeumannomyces infect roots of monocotyledons. Gaeumannomyces graminis contains four varieties, var. tritici, var. avenae, var. graminis, and var. maydis. G. graminis varieties tritici, avenae, and graminis have Phialophora-like anamorphs and, together with the other Gaeumannomyces and Phialophora species found on cereal roots, constitute the Gaeumannomyces-Phialophora complex. Relatedness of a number of Gaeumannomyces and Phialophora isolates was assessed by comparison of DNA sequences of the 18S rRNA gene, the 5.8S rRNA gene, and the internal transcribed spacers (ITS). G. graminis var. tritici, G. graminis var. avenae, and G. graminis var. graminis isolates can be distinguished from each other by nucleotide sequence differences in the ITS regions. The G. graminis var. tritici isolates can be further subdivided into R and N isolates (correlating with ability [R] or inability [N] to infect rye). Phylogenetic analysis of the ITS regions of several oat-infecting G. graminis var. tritici isolates suggests that these isolates are actually more closely related to G. graminis var. avenae. The isolates of Magnaporthe grisea included in the analysis showed a surprising degree of relatedness to members of the Gaeumannomyces-Phialophora complex. G. graminis variety-specific oligonucleotide primers were used in PCRs to amplify DNA from cereal seedlings infected with G. graminis var. tritici or G. graminis var. avenae, and these should be valuable for sensitive detection of pathogenic isolates and for diagnosis of take-all.
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502
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Ortiz-Rivera M, Liu Y, Felder R, Leibowitz MJ. Comparison of coding and spacer region sequences of chromosomal rRNA-coding genes of two sequevars of Pneumocystis carinii. J Eukaryot Microbiol 1995; 42:44-9. [PMID: 7728139 DOI: 10.1111/j.1550-7408.1995.tb01538.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Two distinct sequevars, denoted Pc1 and Pc2, of the opportunistic pathogen Pneumocystis carinii have been previously identified based on the sequence of their 26S rRNA genes, the location of group I self-splicing introns and pulsed field electrophoretic patterns of chromosomal DNA. This study shows that the sequences of 16S and 5.8S rRNA genes also vary between these sequevars, and that greater variation was seen in the internal transcribed spacer regions. Polymerase chain reaction and restriction analysis can distinguish between these sequevars.
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MESH Headings
- Animals
- Base Sequence
- Cloning, Molecular
- DNA, Fungal/genetics
- DNA, Ribosomal/genetics
- Genes, Fungal/genetics
- Genetic Variation/genetics
- Molecular Sequence Data
- Pneumocystis/genetics
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Rats
- Rats, Sprague-Dawley
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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503
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Shih HL, Lin CP, Liou RF, Tzean SS. Complete nucleotide sequence of Beauveria bassiana 5.8s rRNA coding gene and flanking internal transcribed spacers. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1995; 5:381-3. [PMID: 8777317 DOI: 10.3109/10425179509020869] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The nucleotide sequence of two clones of Beauveria bassiana in 5.8s rRNA coding gene and ITS regions were completely sequenced. The overall sequence similarity of these two clones is 96%. The identities of internal transcribed spacer (ITS) regions are 91 % (ITSI) and 100% (ITSII), respectively. Both of 5.8s rRNA sequences have 98% homology.
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504
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LoBuglio KF, Taylor JW. Phylogeny and PCR identification of the human pathogenic fungus Penicillium marneffei. J Clin Microbiol 1995; 33:85-9. [PMID: 7699073 PMCID: PMC227885 DOI: 10.1128/jcm.33.1.85-89.1995] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The phylogenetic position of the human pathogenic fungus Penicillium marneffei was assessed from the nucleotide sequences of the nuclear and mitochondrial ribosomal DNA regions. Phylogenetic analysis determined that P. marneffei is closely related to species of Penicillium subgenus Biverticillium and sexual Talaromyces species with asexual biverticillate Penicillium states. Knowledge of the phylogenetic position of P. marneffei facilitated the design of unique oligonucleotide primers, from the nuclear ribosomal DNA internal transcribed spacer region, for the specific amplification of P. marneffei DNA. These primers were successful at selectively amplifying DNA from six isolates of P. marneffei and excluding the other species tested, which included Penicillium subgenus Biverticillium and Talaromyces species and several well-known fungal pathogens, namely, Aspergillus fumigatus, Coccidioides immitis, Histoplasma capsulatum, and Pneumocystis carinii. The primers that we have developed for the specific amplification of P. marneffei have the potential to be incorporated in a PCR identification system which could be used for the identification of this pathogenic agent from clinical material.
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505
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Lu JJ, Bartlett MS, Shaw MM, Queener SF, Smith JW, Ortiz-Rivera M, Leibowitz MJ, Lee CH. Typing of Pneumocystis carinii strains that infect humans based on nucleotide sequence variations of internal transcribed spacers of rRNA genes. J Clin Microbiol 1994; 32:2904-12. [PMID: 7883876 PMCID: PMC264199 DOI: 10.1128/jcm.32.12.2904-2912.1994] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Small portions of the 18S and the 26S rRNA genes, the entire 5.8S rRNA gene, and internal transcribed spacers ITS1 and ITS2 (located between the 18S and 5.8S rRNA genes and between the 5.8S and 26S rRNA genes, respectively) of Pneumocystis carinii that infect humans were cloned and sequenced. The nucleotide sequences of the 18S, 5.8S, and 26S rRNA genes determined in the study were approximately 90% homologous to those of P. carinii that infect rats, while the sequences of ITS1 and ITS2 of P. carinii from the two different hosts were only 60% homologous. The 18S, 5.8S, and 26S rRNA gene sequences of P. carinii from 15 patient specimens were determined and were found to be identical to each other, whereas the ITS sequences were found to be variable. With the observed sequence variation, it was possible to classify the ITS1 sequences into two types and the ITS2 sequences into three types. P. carinii strains that had the same type of ITS1 sequence could have a different type of ITS2 sequence. On the basis of the sequence types of the two ITS regions, P. carinii from the 15 patients were classified into four groups. P. carinii from three patient specimens were found to contain two different ITS sequence patterns. More surprisingly, one additional specimen was found to have one ITS sequence typical of P. carinii isolates that infect humans and another typical of P. carinii isolates that infect rats. The studies indicate that it is possible to type P. carinii strains on the basis from one patient, suggesting that coinfection with more than one strain of P. carinii may occur in the same patient.
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506
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Srikantha T, Gutell RR, Morrow B, Soll DR. Partial nucleotide sequence of a single ribosomal RNA coding region and secondary structure of the large subunit 25 s rRNA of Candida albicans. Curr Genet 1994; 26:321-8. [PMID: 7882426 DOI: 10.1007/bf00310496] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A rDNA cistron of Candida albicans strain WO-1 was cloned and the ITS1, ITS2, 5.8 s rDNA and 25 s rDNA coding regions sequenced in their entirety. These sequences were compared to those of three related yeast species (Saccharomyces cerevisiae, Saccharomyces carlsbergensis, and Thermomyces lanuginosus), and the 5.8 s rDNA was compared to seven additional 5.8 s rDNAs from organisms ranging in complexity from D. discoideum to H. sapiens. The C. albicans ITS regions are shorter than those of most other eukaryotes. The 25 s and 5.8 s rDNA sequences were folded into a secondary structure model based on comparative methods. In a comparison of regional similarities between the large subunit rDNAs of C. albicans, the three related yeasts and other eukaryotes, it is demonstrated that the additional sequences not present in the E. coli 23 s rDNA are more variable than the regions present in both prokaryotes and eukaryotes.
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MESH Headings
- Animals
- Base Sequence
- Candida albicans/chemistry
- Candida albicans/genetics
- Cloning, Molecular
- DNA, Fungal/genetics
- DNA, Ribosomal/genetics
- Genes, Fungal
- Humans
- Mitosporic Fungi/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5.8S/genetics
- Saccharomyces/genetics
- Saccharomyces cerevisiae/genetics
- Sequence Homology, Nucleic Acid
- Species Specificity
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507
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Henry Y, Wood H, Morrissey JP, Petfalski E, Kearsey S, Tollervey D. The 5′ end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J 1994; 13:2452-63. [PMID: 7515008 PMCID: PMC395111 DOI: 10.1002/j.1460-2075.1994.tb06530.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have developed techniques for the detailed analysis of cis-acting sequences in the pre-rRNA of Saccharomyces cerevisiae and used these to study the processing of internal transcribed spacer 1 (ITS1) leading to the synthesis of 5.8S rRNA. As is the case for many eukaryotes, the 5' end of yeast 5.8S rRNA is heterogeneous; we designate the major, short form 5.8S(S), and the minor form (which is seven or eight nucleotides longer) 5.8S(L). These RNAs do not have a precursor/product relationship, but result from the use of alternative processing pathways. In the major pathway, a previously unidentified processing site in ITS1, designated A3, is cleaved. A 10 nucleotide deletion at site A3 strongly inhibits processing of A3 and the synthesis of 5.8S(S); processing is predominantly transferred to the alternative 5.8S(L) pathway. Site A3 lies 76 nucleotides 5' to the end of 5.8S(S), and acts as an entry site for 5'-->3' exonuclease digestion which generates the 5' end of 5.8S(S). This pathway is inhibited in strains mutant for XRN1p and RAT1p. Both of these proteins have been reported to have 5'-->3' exonuclease activity in vitro. Formation of 5.8S(L) is increased by mutations at A3 in cis or in RAT1p and XRN1p in trans, and is kinetically faster than 5.8S(S) synthesis.
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508
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Abou Elela S, Good L, Melekhovets YF, Nazar RN. Inhibition of protein synthesis by an efficiently expressed mutation in the yeast 5.8S ribosomal RNA. Nucleic Acids Res 1994; 22:686-93. [PMID: 8127718 PMCID: PMC307861 DOI: 10.1093/nar/22.4.686] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Recent studies on the inhibition of protein synthesis by specific anti 5.8S rRNA oligonucleotides strongly suggested that this RNA plays an important role in eukaryotic ribosome function. To evaluate this possibility further, a ribosomal DNA transcription unit from Schizosaccharomyces pombe was cloned into yeast shuttle vectors with copy numbers ranging from 2 to approximately 90 per cell; to allow direct detection of expressed RNA and to disrupt the function of the 5.8S rRNA molecule, a five base insertion was made in a universally conserved GAAC sequence. The altered mobility of the mutant RNA was readily detected by gel electrophoresis and analyses indicated that mutant RNA transcription reflected the ratio of plasmid to endogenous rDNA. The highest copy number plasmid resulted in about 40-50% mutant RNA. This mutant RNA was readily integrated into the ribosome structure resulting in an in vivo ribosome population which was also about 40-50% mutant; the rates of growth and protein synthesis were equally reduced by approximately 40%. A comparable level of inhibition in protein synthesis was demonstrated in vitro and polyribosomal profiles revealed a consistent increase in size. Subsequent RNA analyses indicated a normal distribution of mutant RNA in both monoribosomes and polyribosomes, but elevated tRNA levels in mutant polyribosomes. Additional mutations in alternate GAAC sequences revealed similar but cumulative effects on both protein synthesis and polyribosome profiles. Taken together, these results suggest little or no effect on initiation but provide in vivo evidence of a functional role for the 5.8S rRNA in protein elongation.
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509
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Fan M, Currie BP, Gutell RR, Ragan MA, Casadevall A. The 16S-like, 5.8S and 23S-like rRNAs of the two varieties of Cryptococcus neoformans: sequence, secondary structure, phylogenetic analysis and restriction fragment polymorphisms. JOURNAL OF MEDICAL AND VETERINARY MYCOLOGY : BI-MONTHLY PUBLICATION OF THE INTERNATIONAL SOCIETY FOR HUMAN AND ANIMAL MYCOLOGY 1994; 32:163-80. [PMID: 7525916 DOI: 10.1080/02681219480000231] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The nucleotide sequences of the 16S-like, 5.8S and 23S-like rDNAs from the two varieties of Cryptococcus neoformans, C. neoformans var. neoformans and C. neoformans var. gattii, were determined. The rRNA locus has the typical eukaryote organization of 16S-5.8S-23S with the 16S-like and 5.8S rRNA genes separated by a 124-nucleotide spacer and the 5.8S and 23S-like rRNA genes separated by a 187-nucleotide spacer in each strain. The C. neoformans var. neoformans and C. neoformans var. gattii 16S-like, 5.8S and 23S-like rRNAs are, respectively 1802, 158, and 3358 nucleotides in length and share > 99% nucleotide sequence identity, a finding which strongly supports the present taxonomic classification of two varieties within a species. Comparative structure analysis was used to construct secondary-structure models for the deduced 16S-like and 5.8S-23S-like rRNA sequences, which are similar to those of other fungal rRNAs. The C. neoformans 16S-like and 23S-like rRNA sequences were aligned with other eukaryote sequences based on secondary and higher-order structures predicted by comparative structure analysis for phylogenetic analysis. There was good correspondence between the 16S-like and 23S-like derived phylogenetic trees. The closest known fungal relative is Trichosporon beigelii. Southern blot analysis revealed one C. neoformans strain with two types of DNA repeats coding for rRNA which differed in size by about 1000 bp. Restriction fragment length polymorphisms in the rDNA locus provide useful markers for the study of epidemiology and pathogenesis of C. neoformans infections.
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MESH Headings
- Base Sequence
- Cryptococcus neoformans/genetics
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Species Specificity
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510
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Kasuga T, Woods C, Woodward S, Mitchelson K. Heterobasidion annosum 5.8s ribosomal DNA and internal transcribed spacer sequence: rapid identification of European intersterility groups by ribosomal DNA restriction polymorphism. Curr Genet 1993; 24:433-6. [PMID: 7905365 DOI: 10.1007/bf00351853] [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: 01/27/2023]
Abstract
Using conserved fungal ribosomal gene sequences the internal transcribed spacer (ITS) regions one and two (ITS1, ITS2) and the 5.8s ribosomal RNA gene (rRNA) of Heterobasidion annosum were amplified by the polymerase chain reaction (PCR). The nucleotide sequence was determined in three European intersterility groups (ISG-S, -F and -P). Three sequence variants of the ITS were found in ISG-S isolates. The sequence of the ITS of ISG-F differed by two residues from the major ISG-S sequence variant. The ISG-P sequence differed from ISG-S and ISG-F at 15-16 and 16 residues, respectively. Amplified intergenic spacer elements were informative for ISG fingerprinting following digestion with various 4-cutter restriction endonucleases. All differences in the restriction fragments between the ISGs were because of sequence differences in the ITS regions. The fingerprint patterns of isolates from the same intersterility group but from different European localities were identical. These results show that ribosomal DNA fingerprinting is a rapid technique to identify ISGs in Heterobasidion annosum.
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511
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Mercure S, Rougeau N, Montplaisir S, Lemay G. Complete nucleotide sequence of Candida albicans 5.8S rRNA coding gene and flanking internal transcribed spacers. Nucleic Acids Res 1993; 21:4640. [PMID: 8233804 PMCID: PMC311204 DOI: 10.1093/nar/21.19.4640] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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512
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Wesson DM, Collins FH. Sequence and secondary structure of 5.8S rRNA in the tick, Ixodes scapularis. Nucleic Acids Res 1993; 21:4432. [PMID: 8415023 PMCID: PMC310106 DOI: 10.1093/nar/21.18.4432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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513
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Kenton A, Parokonny AS, Gleba YY, Bennett MD. Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. MOLECULAR & GENERAL GENETICS : MGG 1993; 240:159-69. [PMID: 8355650 DOI: 10.1007/bf00277053] [Citation(s) in RCA: 204] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nicotiana tabacum (2n = 48) is a natural amphidiploid with component genomes S and T. We used non-radioactive in situ hybridization to provide physical chromosome markers for N. tabacum, and to determine the extant species most similar to the S and T genomes. Chromosomes of the S genome hybridized strongly to biotinylated total DNA from N. sylvestris, and showed the same physical localization of a tandemly repeated DNA sequence, HRS 60.1, confirming the close relationship between the S genome and N. sylvestris. Results of dot blot and in situ hybridizations of N. tabacum DNA to biotinylated total genomic DNA from N. tomentosiformis and N. otophora suggested that the T genome may derive from an introgressive hybrid between these two species. Moreover, a comparison of nucleolus-organizing chromosomes revealed that the nucleolus organizer region (NOR) most strongly expressed in N. tabacum had a very similar counterpart in N. otophora. Three different N. tabacum genotypes each had up to 9 homozygous translocations between chromosomes of the S and T genomes. Such translocations, which were either unilateral or reciprocal, demonstrate that intergenomic transfer of DNA has occurred in the amphidiploid, possibly accounting for some results of previous genetic and molecular analyses. Molecular cytogenetics of N. tabacum has identified new chromosome markers, providing a basis for physical gene mapping and showing that the amphidiploid genome has diverged structurally from its ancestral components.
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514
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Beech RN, Strobeck C. Structure of the intergenic spacer region from the ribosomal RNA gene family of white spruce (Picea glauca). PLANT MOLECULAR BIOLOGY 1993; 22:887-892. [PMID: 8358034 DOI: 10.1007/bf00027373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Five genomic clones containing ribosomal DNA repeats from the gymnosperm white spruce (Picea glauca) have been isolated and characterized by restriction enzyme analysis. No nucleotide variation or length variation was detected within the region encoding the ribosomal RNAs. Four clones which contained the intergenic spacer (IGS) region from different rDNA repeats were further characterized to reveal the sub-repeat structure within the IGS. The sub-repeats were unusually long, ranging from 540 to 990 bp but in all other respects the structure of the IGS was very similar to the organization of the IGS from wheat, Drosophila and Xenopus.
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515
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Ritland C, Straus NA. High evolutionary divergence of the 5.8S ribosomal DNA in Mimulus glaucescens (Scrophulariaceae). PLANT MOLECULAR BIOLOGY 1993; 22:691-696. [PMID: 8343604 DOI: 10.1007/bf00047409] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ribosomal DNA sequences for the ITS 1, 5.8S, ITS 2 and adjoining regions of the 18S and 25S were obtained from Mimulus glaucescens (Scrophulariaceae) via cloned PCR products. The spacer sequences were completely unrelated to other plant taxa, although spacer lengths were approximately the same. Interestingly, the Mimulus 5.8S sequence was much more divergent than other higher-plant rDNA sequences. Consideration of the secondary structure of the 5.8S rRNA shows that most of the changes in Mimulus are compensatory and preserve the basic secondary structure of the mature RNA molecule.
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516
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Morales VM, Pelcher LE, Taylor JL. Comparison of the 5.8s rDNA and internal transcribed spacer sequences of isolates of Leptosphaeria maculans from different pathogenicity groups. Curr Genet 1993; 23:490-5. [PMID: 8319307 DOI: 10.1007/bf00312640] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The regions coding for the 5.8s rRNA and the flanking internal transcribed spacers (ITS1 and ITS2) from nine isolates of the blackleg pathogen Leptosphaeria maculans and one isolate of Sclerotinia sclerotiorum were amplified by the polymerase chain reaction and sequenced. Five of the L. maculans isolates were highly virulent to Brassica plants, two were weakly virulent and two were isolated from the cruciferous weed Thlaspi arvense. The 5.8s DNA sequences of all L. maculans isolates were identical. However, there were major differences in both ITS1 and ITS2 sequences that correlated with the pathogenicity grouping. Phylogenetic analysis of the ITS sequences by both parsimony and maximum-likelihood methods indicated that each pathogenicity group was statistically different from each other with the weakly-virulent isolates being more closely related to the Thlaspi than to the highly-virulent isolates. The relationships of L. maculans to other fungi, based on a comparison of the 5.8s rDNA sequences, are discussed.
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517
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Kasuga T, Mitchelson K. Determination of the DNA sequence of the 5.8S ribosomal gene of Heterobasidion annosum and Heterobasidion araucariae. Nucleic Acids Res 1993; 21:1320. [PMID: 8464717 PMCID: PMC309303 DOI: 10.1093/nar/21.5.1320] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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518
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Ruiz-Sala P, Pérez-González JA, Ramón D. Nucleotide sequence of a Trichoderma longibrachiatum DNA fragment encoding the 5.8S rRNA gene. Nucleic Acids Res 1993; 21:741. [PMID: 8441683 PMCID: PMC309177 DOI: 10.1093/nar/21.3.741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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519
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Anderson GR, Barker SC. Species differentiation in the Didymozoidae (Digenea): restriction fragment length differences in internal transcribed spacer and 5.8S ribosomal DNA. Int J Parasitol 1993; 23:133-6. [PMID: 8096835 DOI: 10.1016/0020-7519(93)90106-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Genetic differences among six didymozoid species distinguished on morphological criteria (Didymozoon species A, B, E, F and G, and Neometadidymozoon helicis) were sought by restriction fragment length analysis of internal transcribed spacer (ITS) and 5.8S ribosomal DNA. DNA fragments comprising ITS1, 5.8S and ITS2 were amplified by polymerase chain reaction for each of the six species. Digestion with the restriction enzyme (RE) Rsa I yielded four to six fragments, approximately 65-775 base pairs long. Digestion with another RE, Sau 3AI, yielded five to eight fragments, approximately 25-775 base pairs long. No intraspecific variation was detected but there were many interspecific differences. All six species distinguished by morphology are genetically distinct. Thus, the reliability of the morphological characters originally used to separate the species was confirmed.
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520
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Cevallos MA, Porta H, Alagón AC, Lizardi PM. Sequence of the 5.8S ribosomal gene of pathogenic and non-pathogenic isolates of Entamoeba histolytica. Nucleic Acids Res 1993; 21:355. [PMID: 8441643 PMCID: PMC309116 DOI: 10.1093/nar/21.2.355] [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: 01/30/2023] Open
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521
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Yeh LC, Lee JC. Structure analysis of the 5' external transcribed spacer of the precursor ribosomal RNA from Saccharomyces cerevisiae. J Mol Biol 1992; 228:827-39. [PMID: 1469716 DOI: 10.1016/0022-2836(92)90867-j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Full-length precursor ribosomal RNA molecules were produced in vitro using as a template, a plasmid containing the yeast 35 S pre-rRNA gene under the control of the phage T3 promoter. The higher-order structure of the 5'-external transcribed spacer (5' ETS) sequence in the 35S pre-rRNA molecule was studied using dimethylsulfate, 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluenesulfonate, RNase T1 and RNase V1 as structure-sensitive probes. Modified residues were detected by primer extension. Data produced were used to evaluate several theoretical structure models predicted by minimum free-energy calculations. A model for the entire 5'ETS region is proposed that accommodates 82% of the residues experimentally shown to be in either base-paired or single-stranded structure in the correct configuration. The model contains a high degree of secondary structure with ten stable hairpins of varying lengths and stabilities. The hairpins are composed of the Watson-Crick A.T and G.C pairs plus the non-canonical G.U pairs. Based on a comparative analysis of the 5' ETS sequence from Saccharomyces cerevisiae and Schizosaccharomyces pombe, most of the base-paired regions in the proposed model appear to be phylogenetically supported. The two sites previously shown to be crosslinked to U3 snRNA as well as the previously proposed recognition site for processing and one of the early processing site (based on sequence homology to the vertebrate ETS cleavage site) are located in single-stranded regions in the model. The present folding model for the 5' ETS in the 35 S pre-rRNA molecule should be useful in the investigations of the structure, function and processing of pre-rRNA.
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MESH Headings
- Base Sequence
- CME-Carbodiimide/analogs & derivatives
- Carbodiimides/pharmacology
- Cross-Linking Reagents
- DNA, Recombinant
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA Precursors/drug effects
- RNA Precursors/genetics
- RNA Processing, Post-Transcriptional
- RNA, Fungal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Ribonucleases/pharmacology
- Saccharomyces cerevisiae/genetics
- Sequence Analysis, RNA
- Sulfuric Acid Esters/pharmacology
- Transcription, Genetic
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522
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Suh Y, Thien LB, Zimmer EA. Nucleotide sequences of the internal transcribed spacers and 5.8S rRNA gene in Canella winterana (Magnoliales; Canellaceae). Nucleic Acids Res 1992; 20:6101-2. [PMID: 1461743 PMCID: PMC334481 DOI: 10.1093/nar/20.22.6101] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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523
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Aimi T, Yamada T, Murooka Y. Nucleotide sequence and secondary structure of 5.8S rRNA from the unicellular green alga, Chlorella ellipsoidea. Nucleic Acids Res 1992; 20:6098. [PMID: 1461741 PMCID: PMC334479 DOI: 10.1093/nar/20.22.6098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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524
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Abstract
We report here the isolation and identification of the RNA specifically immunoprecipitated and covalently linked to the tumor suppressor gene product p53. After treatment with proteinase K, the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) band of p53 yields a single, discrete 157-nucleotide RNA, which was cloned, sequenced, and identified as 5.8S rRNA. 5.8S rRNA was obtained only after proteolysis of the p53 SDS-PAGE band. Free 5.8S rRNA did not comigrate with p53 in SDS-PAGE. This RNA was only immunoprecipitated from cells containing p53. Protein-free RNA obtained by proteolysis of the p53 band hybridized to the single-stranded DNA vector containing the antisense sequence of 5.8S rRNA. The covalence of the p53-5.8S rRNA linkage was demonstrated by the following findings: (i) p53 and the linked 5.8S rRNA comigrated in SDS-PAGE; (ii) only after treatment of the p53-RNA complex with proteinase K did the 5.8S rRNA migrate differently from p53-linked 5.8S rRNA; and (iii) this isolated RNA was found linked to phosphoserine, presumably at the 5' end. Covalent linkage to the single, specific RNA suggests that p53 may be involved in regulating the expression or function of 5.8S rRNA.
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525
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Lin H, Niu MT, Yoganathan T, Buck GA. Characterization of the rRNA-encoding genes and transcripts, and a group-I self-splicing intron in Pneumocystis carinii. Gene X 1992; 119:163-73. [PMID: 1398096 DOI: 10.1016/0378-1119(92)90268-t] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although Pneumocystis carinii is the most common opportunistic pathogen infecting individuals with AIDS, very little is known of the basic biology of the organism. We have examined the ribosomal RNA (rRNA) and the DNA encoding it (rDNA) in P. carinii in an attempt to clarify its taxonomic position and to begin to study its genetic processes. Electrophoretic analysis showed that the sizes of the P. carinii rRNAs are quite similar to the sizes of the corresponding rRNAs from Saccharomyces cerevisiae. Direct sequence analysis of approx. 60% of the 18S small subunit-rRNA (Ss-rRNA) confirmed that its sequence is similar to that of yeast-like fungi and that a putative group-I intron previously observed in the 18S rDNA is, in fact, excised from the mature rRNA. PCR analysis of the intron in P. carinii genomic DNA showed that each of the multiple rDNA genes bears the group-I intron and in vitro transcripts of the intron autocatalytically excise from the rRNA primary transcript in the presence of GTP. Finally, analogues of GTP inhibit the self-splicing reaction, indicating that the guanosine-binding site of the intron closely resembles that of other well-characterized group-I introns. Since no group-I introns have been found in higher eukaryotes, this self-splicing process represents a viable target for chemotherapy of P. carinii pneumonia (PCP).
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MESH Headings
- Antifungal Agents/pharmacology
- Base Sequence
- Binding, Competitive
- Cloning, Molecular
- DNA, Fungal
- Guanosine/metabolism
- Introns
- Molecular Sequence Data
- Nucleic Acid Conformation
- Pneumocystis/genetics
- Polymerase Chain Reaction
- RNA Splicing
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5S/genetics
- Transcription, Genetic
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