Showing papers on "Ribosomal DNA published in 1987"

Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer.

Abstract: Ribosomal RNA genes in plants are highly variable both in copy number and in intergenic spacer (IGS) length. This variability exists not only between distantly related species, but among members of the same genus and also among members of the same population of a single species. Analysis of inheritance indicates that copy number change is rapid, occurring even among somatic cells of individual plants, and that up to 90% or more of the gene copies are superfluous. Subrepetitive sequences within the IGS appear to be changing rapidly as well. They are not only variable in sequence from one species to the next, but can vary in number between neighboring gene repeats on the chromosome. In all species examined in detail they are located in the same region of the IGS and contain sequences that can be folded into stem-loop structures flanked by a pyrimidine-rich region. It has been suggested that these subrepeats function in transcriptional enhancement, termination or processing, or in recombination events generating the high multiplicity of ribosomal genes.

Strain and species identification by restriction fragment length polymorphisms in the ribosomal DNA repeat of Candida species.

Abstract: Restriction fragment length polymorphisms in the ribosomal DNA (rDNA) have been shown to be a useful criterion for distinguishing among various isolates of Candida albicans. In a sample of 12 clinical isolates, we found six different classes based on variations in the fragments produced from genomic DNA by EcoRI and visualized after Southern transfer by being probed with a plasmid containing Saccharomyces cerevisiae rDNA. Some of the classes appeared to be heterozygous at the rDNA locus. Similar digestion of other Candida species showed that each could be identified on the basis of its restriction patterns. Since these are highly reiterated genes, the differences were apparent on ethidium bromide-stained gels; Southern transfers were not necessary. EcoRI restriction maps of the rDNA of C. albicans, C. stellatoidea, C. tropicalis, and C. guilliermondii were determined.

Structure and variation in ribosomal RNA genes of pea : Characterization of a cloned rDNA repeat and chromosomal rDNA variants.

Abstract: A complete ribosomal DNA (rDNA) repeat unit has been cloned from the genome of Pisum sativum (garden pea) and used to construct a map containing a total of 58 cleavage sites for 23 different restriction enzymes. Regions encoding 18s and 25s ribosomal RNA (rRNA) were identified by R-loop analysis. A 180 bp sequence element is repeated eight times in the intergenic ‘nontranscribed spacer’ (NTS) region, as defined by eight evenly spaced RsaI cleavage sites. Sequence heterogeneity among these elements (subrepeats) is indicated by the presence of an NcoI site within the five RsaI subrepeats distal to the 25s rRNA gene but not in the three subrepeats proximal to this gene, and also by the presence of an additional RsaI cleavage site in one subrepeat.

Relatedness of strains of Fusarium oxysporum from crucifers measured by examination of mitochondrial and ribosomal DNA

Abstract: Kistler, H. C., Bosland, P. W., Benny, U., Leong, S., and Williams, P. H. 1987. Relatedness of strains of Fusarium oxysporum from crucifers measured by examination of mitochondrial and ribosomal DNA. Phytopathology 77:1289-1293. DNA was examined from 25 isolates representing three formae speciales among isolates regardless of pathotype or geographic origin. RFLPs were of Fusarium oxysporum from crucifers. The restriction enzyme fragment detected in mtDNA, and these corresponded directly with forma specialis. patterns of mitochondrial DNA (mtDNA) and nuclear ribosomal DNA A unique mtDNA restriction enzyme fragment pattern was detected in one (rDNA) were compared among isolates to examine phylogenetic isolate from Japan, indicating that geographical divergence is present in the relationships among pathotypes and to determine whether any restriction pathogen population. All isolates examined contained plasmid-like DNA fragment-length polymorphisms (RFLPs) were associated with geographic (plDNA). Three different plDNAs were detected and were also correlated origin. No differences in rDNA restriction fragment patterns were seen with forma specialis. The phytopathogenic fungus, Fusarium oxysporum Schlecht. MATERIALS AND METHODS emend. Snyd. & Hans., causes the wilt or yellows disease of crucifers worldwide. Pathotypic variation of F. oxysporum on crucifers has been categorized into the formae speciales Fungal strains. Twenty-five virulent isolates of the three crucifer conglutinans, raphani, and matthioli based on the host species formae speciales representing diverse geographic origins and all Brassica oleracea L., Raphanus sativus L., and Matthiola incana known pathotypes were included (Table 1). Isolates were main(L.) R. Br., respectively (2). Further differentiation into races is tained in sterile soil at 4 C until studied. (In previous publications based on differential pathogenicity within a forma specialis. A [e.g., 8,12], F. o. f. sp. conglutinans races 1 and 2, F. o. f. sp. correspondence of forma specialis with isozyme polymorphism raphani, and F. o. f. sp. matthioli races I and 2 were referred to as and vegetative compatibility exists even among isolates from F. o. f. sp. conglutinans races 1, 5, 2, 3, and 4, respectively.) diverse geographic regions (2). In addition, two unique linear A strain of F. o. f. sp. lycopersici race 1 and a homothallic strain mitochondrial plasmid-like DNAs (plDNAs) are found in F. of Nectria haematococca Berk & Br. (from F. Cervone and oxysporum strains that infect Brassica and Raphanus, and the D. Parisot, respectively) were maintained in 50% glycerol at-80 C. presence of these plDNAs is correlated to the host range of the Isolation of DNA. Mycelium was grown in 1 L of potatofungus (8). dextrose broth (Difco, Detroit, MI) that was gyrated at 125 rpm Biological variation can be studied at the level of DNA for 5-7 days at 24 C. The mycelium was filtered through a double sequences by comparing restriction endonuclease fragments. layer of cheesecloth, frozen, and lyophilized. Studies of mitochondrial DNA (mtDNA) from Aspergillus, Fungal DNA extractions were carried out by a modified method Claviceps, Cochliobolus, Neurospora, and Penicillium (4,7,9 of Specht et al (15) that was described previously (8). Plasmid 14,16) have demonstrated variation as determined by restriction DNA grown in Escherichia coli strain H B101 was obtained by the enzyme fragment-length polymorphisms (RFLPs). RFLPs have alkali lysis method (10). DNA from Magnaporthe grisea Cavara also been detected in the tandemly repeated nuclear genes for was provided by Masatoki Taga (Sakata Seed Co.). ribosomal RNA (rDNA) in Cachijobolus and Neurospora (7,13). Restriction endonuclease analysis. Approximately 0.25 pzg of The small size of mtDNA and rDNA makes them suitable for DNA was digested with restriction enzymes as recommended by restriction enzyme analysis. Thus, restriction site polymorphism the manufacturer (Bethesda Research Laboratories, Inc., provides yet another way to investigate molecular evolution of Gaithersburg, MD, or Promega Biotec, Madison, WI). Restriction conspecific populations. Because of the rapid rate of evolution of fragments were separated by horizontal agarose gel electrophoresis mtDNA, which is estimated in animals to be 10 times faster than (0.7% agarose), using Tris/borate buffer (10) and a potential that of nuclear DNA (3), analysis of mtDNA may provide a more gradient of 1-5 V cm-'. DNA was detected by staining gels in a sensitive measure of divergence in populations than other solution of ethidium bromide (0.5 /Ag ml-') followed by UV transmethods. illumination. Lambda phage DNA (Promega Biotec) cut by Hind III or Hind III and Bgl II restriction endonuclease was used for size markers. DNA was denatured, transferred to nitrocellulose, and hybridized to 32p-labelled DNA probes as previously described This article is in the public domain and not copyrightable. It may be freely (10). Nick translations of DNA (0.1 Mg) used as probes were reprinted with customary crediting of the source. The American performed by standard methods (10) to give specific activities of Phytopathological Society, 1987. >5X 10 7 dpm •g-1 Vol. 77, No. 9,1987 1289 DNA manipulations. DNA from mitochondrial fractions was digested with restriction enzyme Eco RI and ligated with E. coli 1 2 3 4 5 6 7 8 9 101 112 13 plasmid pUCI9 (18), which had been linearized with the same endonuclease. Ligations were used to transform E. coli strain TB 1, a rk Mk derivative of JM83 (18). Plasmid DNA of Ampr, LacTABLE 1. Isolates of Fusarium oxysporum from crucifers used in this study PH W# Pathotype' Origin Host species 2 Foc I Florida Brassica oleracea 81 FocI Wisconsin B. oleracea 684 Foc2 California B. oleracea 699 For Wisconsin Raphanus sativus 719 Foci Hungary B. oleracea 722 Foc I ATCC 9990c B. oleracea 723 FocI ATCC 16600 B. oleracea 724 For ATCC 16601 R. sativus 725 Fom I ATCC 16602 Matthiola incana 726 Fom2 ATCC 16603 M. incana 760 For Germany R. sativus Fig. 2. Autoradiogram showing ribosomal DNA digested with Sau 3A. 768 Foc I Wisconsin B. oleracea Total nuclear DNA was digested to completion with endonuclease Sau 3A 777 Foci Japan B. oleracea and fractionated on a 1.5% agarose gel. Southern blot of that gel was 781 Fom I Japan M. incana hybridized with 32p-labelled pMF2, the cloned Neurospora rDNA. Lanes 793 FomI CBS 247.61' M. incana contain DNA from 1) PHW 722,2) PHW 723, 3) PHW 724,4) PHW 725, 795 For CBS 262.50 R. sativus 5) PHW 760, 6) PHW 768, 7) PHW 781, 8) PHW 793, 9) PHW 796, 10) 796 For CBS 488.67 ? PHW 806, 11) F. o. f. sp. lycopersici, 12) Magnaporthe grisea, and 13) 806 FomI Italy M. incana Nectria haematococca. 808 Foc2 California B. oleracea 809 Foc2 California B. oleracea 811 Foc2 California B. oleracea q 0 D r, C. 815 For France R. sativus 821 For Taiwan R. sativus 1088 For Japan R. sativus 1094 Fom I Japan M. incana 'PHW Laboratory designations of isolates maintained by Paul H. Williams, Department of Plant Pathology, University of WisconsinMadison 53706. b Foc i = F. o. f. sp. conglutinans race 1; Foc2 = F. o. f. sp. conglutinans race 2; For = F. o. f. sp. raphani; Fom I F. o. f. sp. matthioli race 1; Fom2 = F. o. f. sp. matthioli race 2. CATCC = American Type Culture Collection, Rockville, MD. 1 . 9 dCBS Centraalbureau voor Schemmelcultures, Baarn, Netherlands.

The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme

Abstract: Two classes of DNA elements interrupt a fraction of the rRNA repeats of Bombyx mori. We have analyzed by genomic blotting and sequence analysis one class of these elements which we have named R2. These elements occupy approximately 9% of the rDNA units of B. mori and appear to be homologous to the type II rDNA insertions detected in Drosophila melanogaster. Approximately 25 copies of R2 exist within the B. mori genome, of which at least 20 are located at a precise location within otherwise typical rDNA units. Nucleotide sequence analysis has revealed that the 4.2-kilobase-pair R2 element has a single large open reading frame, occupying over 82% of the total length of the element. The central region of this 1,151-amino-acid open reading frame shows homology to the reverse transcriptase enzymes found in retroviruses and certain transposable elements. Amino acid homology of this region is highest to the mobile line 1 elements of mammals, followed by the mitochondrial type II introns of fungi, and the pol gene of retroviruses. Less homology exists with transposable elements of D. melanogaster and Saccharomyces cerevisiae. Two additional regions of sequence homology between L1 and R2 elements were also found outside the reverse transcriptase region. We suggest that the R2 elements are retrotransposons that are site specific in their insertion into the genome. Such mobility would enable these elements to occupy a small fraction of the rDNA units of B. mori despite their continual elimination from the rDNA locus by sequence turnover.

Analysis of the Brassica oleracea genome by the generation of B. campestris-oleracea chromosome addition lines: characterization by isozymes and rDNA genes

Abstract: This study aimed at generating chromosome addition lines and disclosing genome specific markers in Brassica. These stocks will be used to study genome evolution in Brassica oleracea L., B. campestris L. and the derived amphidiploid species B. napus L. B. campestris-oleracea monosomic and disomic chromosome addition plants were generated by crossing and backcrossing the natural amphidiploid B. napus to the diploid parental species B. campestris. The pollen viability of the derived sesquidiploid and hyperploid ranged from 63% to 88%, while the monosomic and disomic addition plants had an average pollen fertility of 94% and 91%, respectively. The addition lines were genetically characterized by genome specific markers. The isozymes for 6PGD, LAP, PGI and PGM, and rDNA Eco RI restriction fragments were found to possess the desired genome specificity. Duplicated loci for several of these markers were observed in B. campestris and B. oleracea, supporting the hypothesis that these diploid species are actually secondary polyploids. A total of eight monosomic and eight disomic addition plants were identified and characterized on the basis of these markers. Another 51 plants remained uncharacterized due to the lack of additional markers. rDNA genes were found to be distributed in more than one chromosome, differing in its restriction sites. Intergenomic recombination for some of the markers was detected at frequencies between 6% and 20%, revealing the feasibility of intergenomic gene transfer.

An unusually compact ribosomal DNA repeat in the protozoan Giardia lamblia

Abstract: The ribosomal RNA (rRNA) genes of the protozoan parasite Giardia lamblia have been analyzed with respect to size, composition and copy number They are found to be remarkable in several respects First, the rRNAs themselves are the smallest yet reported for any eukaryotic organism Second, the genes encoding them are found as an exceptionally small tandemly repeated unit of only 54 kilobase-pairs Third, the genes are extraordinarily G:C rich, even in regions which are highly conserved between all other eukaryotic rRNA genes Finally, by analogy to other organisms, the 58S RNA appears to lack about 15 nucleotides from its 3'-end, a region previously thought to be essential for 58S RNA function We also provide the first estimates of the genomic complexity and total G:C content of this important protozoan pathogen

Heritability and Variability in Ribosomal RNA Genes of Vicia faba

Abstract: We have compared the restriction patterns and copy numbers of ribosomal RNA genes (rDNA) between and within individuals of Vicia faba . While the EcoRI blot-hybridization patterns changed only after one to two generations, copy number changes were found among different tissues of the same plant. Copy number differences among individuals in the population were as great as 95-fold, whereas as much as a 12-fold variation was seen among tissues of the same plant. Among individual F(1) progeny from genetic crosses, nearly an 8-fold variation was seen, and among individuals of the F(2) generation a spread of 22-fold was measured. Among individual siblings of self-pollinated parents, up to 7-fold variation was observed. However, changes in copy number did not necessarily indicate changes in rDNA EcoRI blot-hybridization pattern, and vice versa. Furthermore, nearest neighbor analysis of R-loop experiments showed that the arrangement of members of the "nontranscribed" spacer (NTS) size classes along the chromosome was not random, but some clustering was indicated. The data are consistent with the hypothesis that sister chromatid exchange in somatic cells of V. faba is the primary mechanism for altering the rDNA copy number as well as causing the extreme variation observed in the NTS. Variation among individuals in rDNA blot-hybridization pattern was also observed for Vicia villosa, Vicia dasycarpa, Vicia benghalensis and Vicia pannonica.

Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata

Abstract: In Crithidia fasciculata, a trypanosomatid protozoan, the nuclear-encoded `28S' rRNA is multiply fragmented, comprising two large (c and d) and four small (e, f, g and j) RNA species. We have determined that the coding sequences for these RNAs (and that of the 5.8S rRNA, species i) are separated from one another by spacer sequences ranging in size from 31 to 416 bp. Coding and spacer sequences are presumably co-transcribed, with excision of the latter during post-transcriptional processing generating a highly fragmented large subunit (LSU) rRNA. Secondary structure modelling indicates that the C. fasciculata LSU rRNA complex (seven segments, including 5.8S rRNA) is held together in part by long-range intermolecular base pairing interactions that are characteristic of intramolecular interactions in the covalently continuous LSU (23S) rRNA of Escherichia coli. At least one functionally critical region (encompassing the α-sarcin cleavage site) is contained in a small RNA species (f) rather than in one of the two large RNAs. Within a proposed secondary structure model of C. fasciculata LSU rRNA, discontinuities between the different segments (created by spacer excision) map to regions that are highly variable in structure in covalently continuous LSU rRNAs. We suggest that `rRNA genes in pieces' and discontinuous rRNAs may represent an evolutionarily ancient pattern.

Clones of human ribosomal DNA containing the complete 18 S-rRNA and 28 S-rRNA genes. Characterization, a detailed map of the human ribosomal transcription unit and diversity among clones.

Abstract: We have isolated several new clones of human ribosomal DNA. Each clone contains part of the external transcribed spacer, a complete 18 S-rRNA gene, the internal transcribed spacers, a complete 28 S-rRNA gene and a short downstream flanking region. We present a detailed map of the human ribosomal transcription unit with the locations of numerous useful restriction sites. In particular, a unique NheI site in the 5.8 S-rRNA gene enabled this gene to be mapped with respect to the 18 S-rRNA and 28 S-rRNA genes. The human 45 S-rRNA coding region is approx. 13,000 nucleotide residues long, of which the external transcribed spacer comprises approx. 3700 nucleotide residues and the first and second internal transcribed spacers comprise approx. 1070 and 1200 nucleotide residues respectively. A partial survey for sites of variation between clones has revealed a single point of variation among 18 S-rRNA gene sequences (a T/C variation at position 140), several sites of length variation in the regions of the transcribed spacers closely flanking the 18 S-rRNA genes, and some sites of length variation among 28 S-rRNA genes. Most of these sites of variation are associated with simple sequence tracts and are in regions that are known to undergo relatively rapid evolutionary divergence. In particular, the sites of variation among 28 S-rRNA genes occur in G + C-rich tracts whose lengths vary among vertebrates and that can be correlated with extensive hairpin structures previously observed by electron microscopy. Each of the clones so far surveyed in detail differs from the others in one or more respects.

rRNA genes of Naegleria gruberi are carried exclusively on a 14-kilobase-pair plasmid.

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.

Chromosome banding in amphibia. XI. Constitutive heterochromatin, nucleolus organizers, 18S + 28S and 5S ribosomal RNA genes in Ascaphidae, Pipidae, Discoglossidae and Pelobatidae.

Abstract: The karyotypes of 14 species of Anura from 9 genera of the suborders Amphicoela, Aglossa, Opisthocoela and Anomocoela were analysed with various banding techniques and conventional cytogenetic methods. The 18S + 28S and 5S ribosomal RNA genes were localized by means of in situ hybridization. No Q-, R- and G-banding patterns in the euchromatic segments of the metaphase chromosomes could be demonstrated in any of the species; this does not seem to be caused by a higher degree of spiralization of the amphibian chromosomes, but by the special DNA organization in these organisms. In most karyotypes, constitutive heterochromatin is present at centromeres, telomeres and nucleolus organizer regions (NORs), but rarely in interstitial positions. The heterochromatic regions are either quinacrine positive and mithramycin negative or vice versa. All species examined possess only one homologous pair of NORs: these display the brightest mithramycin fluorescence in the karyotypes. Many specimens exhibited unequal labelling of the two NORs both after silver and mithramycin staining as well as after in situ hybridization with 3H-18S + 28S rRNA. In four species, between one and six chromosome pairs with homologous 5S rRNA sites could be identified. The 5S rRNA genes and the 18S + 28S rRNA genes are closely linked in two species. In the male meiosis of the Amphicoela and Opisthocoela, there are intersitial, subterminal and terminal chiasmata in the bivalents, whereas only terminal chiasmata are observed in the bivalents of the Aglossa and Anomocoela. No heteromorphic sex-specific chromosomes could be demonstrated in any of the species. The differential staining techniques revealed that the chromosomal structure in these four suborders is largely the same as in the highly evolved anuran suborders Procoela and Diplasiocoela.

Population subdivision for ribosomal dna repeat variants in clematis fremontii

Abstract: Recent studies have documented a wide range of kinds and levels ofvariation in DNA sequences among the individual members of populations. The discovery of high levels of variation, particularly in the midrepetitive multigene family ofribosomal DNA (rDNA), has stimulated a great deal of interest in delineating both the forces which generate this variability and those which affect its distribution. Opinions vary as to the relative importance of molecular phenomena, including those responsible for molecular drive (Dover, 1982), versus populational phenomena, such as selection or genetic drift. Here we document genetic subdivision for rDNA spacer length variants among members of a population of a native plant, Clematis fremontii (Ranunculaceae), and suggest that genetic drift within subpopulations may be a predominant force influencing the distribution of such variation. Clematisfremontii is a long-lived perennial forb endemic to portions ofthe mixed-grass prairies ofKansas and to dolomitic glades in the Ozark plateau of Missouri. The prairie and glade populations have been given distinction at the subspecific level (Erickson, 1943); our work here is with a glade population, subspecies riehlii. These glades are prairie remnants which presumably have been isolated since the end of the mid-Holocene Hypsithermal Interval about 5,000 years ago (Delcourt and Delcourt, 1981; King, 1981). Glade populations currently form an island-like system in the surrounding forest. C. fremontii has a mixed system of mating (Erickson, 1945), although the precise frequency of selfing is not known. Analysis of the spatial distribution ofleaf shape within single glades suggests that populations of C. fremontii are genetically subdivided (Erickson, 1945). The distribution of molecular variation within a population is currently being studied by an analysis of rDNA, the set of nuclear genes which encode three of the ribosomal RNA components of cytoplasmic ribosomes. These genes, which are transcribed as a single unit, are found as clusters of tandemly repeated segments. Adjacent transcription units are separated by a nontranscribed spacer (NTS). A single transcription unit and an NTS comprise a single repeat unit. Figure IA shows the location of various coding and noncoding portions of an rDNA repeat. The rectangles represent the 17S, 5.8S, and 26S coding regions. Lines represent spacer regions which are not seen as mature rRNA species. rDNA repeats have been shown to vary in length in a number of plant species (Delseny et aI., 1979; Oono and Sugiura, 1980; Appels et aI., 1980; Yakura et aI., 1983, 1984; Doyle and Beachy, 1985), and this variability corresponds in most cases to length differences in the NTS. In this study we analyze the spatial pattern oflength variation along a transect within a glade population of C. fremontii.

Correlations between development rates, enzyme activities, ribosomal DNA spacer-length phenotypes, and adaptation in Drosophila melanogaster.

Abstract: Selection for "fast" preadult development rate among the progeny of flies collected in a natural population of Drosophila melanogaster produced a line that developed more rapidly than a line selected for "slow" preadult development rate. Assays for enzyme activity levels showed that the activities of alpha-glycerophosphate dehydrogenase, alcohol dehydrogenase, and malic enzyme were higher in the fast than in the slow line, but that the activity of superoxide dismutase was lower in the fast line. Differences in the frequencies of spacer-length phenotypes of X chromosome-linked rRNA genes (rDNA), which developed between the lines during the selection process, are larger than can be explained on the basis of genetic drift alone. Long rDNA spacers had high frequency in the fast line; short spacers, in the slow line. We conclude that enzyme levels affected adaptation under the selective regimes imposed and that the different X-linked rDNA spacer-length phenotypes are either adaptive in themselves or that they mark chromosomal segments carrying genes relevant to adaptation.

Putative promoter elements for the ribosomal RNA genes of the thermoacidophilic archaebacterium Sulfolobus sp. strain B12

Abstract: In Sulfolobus sp. strain B12, single-copy genes encode the three ribosomal RNAs. The genes for the 16S rRNA and for the 23S rRNA are closely linked but separated from the 5S rRNA gene. Transcription of the 16S/23S rRNA gene cluster starts 139 nucleotides upstream of the 5'-end of mature 16S rRNA. For the 5S rRNA gene the point of transcription initiation coincides with the 5'-end of mature 5S rRNA. The comparison of the upstream regions for these transcriptional start sites shows the presence of a completely conserved trinucleotide sequence around the point of transcription initiation and a completely conserved octanucleotide sequence about 22 nucleotides upstream of it. These sequences are only moderately homologous to putative promoter elements for stable RNA genes in the closely related archaebacterium Thermoproteus tenax (1), but they are very similar to corresponding sequences in the distantly related archaebacterium Methanococcus vannielii (2). The consensus sequence found for Sulfolobus and Methanococcus could therefore constitute the archetype of an archaebacterial promoter for stable RNA genes.

Evolution of the ribosomal DNA spacers of Drosophila melanogaster: different patterns of variation on X and Y chromosomes.

Abstract: Length variation of the ribosomal gene spacers of Drosophila melanogaster was studied. Analysis of 47 X chromosomal and 47 Y chromosomal linked rDNA arrays collected from five continents indicates that the arrays on the two chromosomes differ qualitatively. The Y-linked arrays from around the world share little or no similarity for either their overall length or the organization of their spacers. Most of the X-linked arrays do, however, share a major length spacer of 5.1 kb. In addition, those X-linked arrays that have a major 5.1-kb band have similar spacer organization as demonstrated by genomic DNA digestions with several restriction enzymes. These data strongly support the hypothesis that spacer length patterns on only X-linked genes are maintained primarily by natural selection.

Identification of Campylobacter species by southern hybridization of genomic DNA using an oligonucleotide probe for 16S rRNA genes

Abstract: Nine strains of four species of Campylobacter (C. jejuni, C. fetus, C. coli, C. laridis) were studied by genomic Southern hybridization. Restriction digests of chromosomal DNA prepared by treatment with either Eco RV or Rsa I were probed with an oligonucleotide specific for Campylobacter 16S ribosomal RNA genes. Six distinct hybridization patterns were obtained, each indicating the presence of 2–4 copies of the 16S rRNA gene are encoded in Campylobacter DNA. Differences in the hybridization patterns were observed not only between members of two species, but also between individual strains of the same species. Of the four C. jejuni strains tested, two different hybridization patterns were evident. Similar results were observed with different strains of C. coli and C. laridis. The relative simplicity of the patterns obtained, combined with the apparent diversity among individual strains, suggests that DNA-fingerprinting with the 16S rRNA gene probe could be a potentially useful identification method in epidemiological studies of Campylobacter infection.

Variability and genetics of spacer DNA sequences between the ribosomal-RNA genes of hexaploid wheat (Triticum aestivum)

Abstract: Using restriction enzyme digests of genomic DNA extracted from the leaves of 25 hexaploid wheat (Triticum aestivum L. em. Thell.) cultivars and their hybrids, restriction fragment length polymorphisms of the spacer DNA which separates the ribosomal-RNA genes have been examined. (From one to three thousand of these genes are borne on chromosomes 1B and 6B of hexaploid wheat). The data show that there are three distinct alleles of the 1B locus, designated Nor-B1a, Nor-B1b, and Nor-B1c, and at least five allelic variants of the 6B locus, designated Nor-B2a, Nor-B2b, Nor-B2c, Nor-B2d, and Nor-B2e. A further, previously reported allele on 6B has been named Nor-B2f. Chromosome 5D has only one allelic variant, Nor-D3. Whereas the major spacer variants of the 1B alleles apparently differ by the loss or gain of one or two of the 133 bp sub-repeat units within the spacer DNA, the 6B allelic variants show major differences in their compositions and lengths. This may be related to the greater number of rDNA repeat units at this locus. The practical implications of these differences and their application to wheat breeding are discussed.

Ribosomal DNA (rDNA) spacer polymorphism in mole rats.

Abstract: Genetic differentiation of ribosomal DNA (rDNA) nontranscribed-spacer (NTS) polymorphism was analyzed in 50 individuals from 13 populations among the four chromosomal species (2n = 52, 2n = 54, 2n = 58, and 2n = 60) of subterranean mole rats of the Spalax ehrenbergi complex in Israel. Southern blot analysis with a mouse rDNA probe and two restriction enzymes, EcoRI and BamHI, revealed various sizes of major restriction fragments. The assumption that this variation is due to length polymorphism of NTS DNA was supported by the construction of restriction-site maps. On the basis of the EcoRI and BamHi fragment lengths, we could characterize the major types of NTS rDNA repeating units in each individual. Each member of the central population in the four chromosomal groups of mole rats has a characteristic combination of the NTS types, suggesting that the karyotype groups were genetically diverged. Some near-hybrid-zone populations reflect similarities with the rDNA spectra of a neighbor chromosomal group. This might have resulted from gene flow across the hybrid zones.

Immunocytochemical localization of RNA polymerase I in the fibrillar centers of nucleoli

Abstract: For an understanding of the functional organization of the nucleolus identification of the site of the expression of the rRNA genes is of considerable importance. Although various stages of preribosome formation have been mapped to morphologically distinct components of the nucleolus (Hadjiolov, 1985), the intranucleolar location of transcriptionally active rRNA genes has remained uncertain. From high resolution autoradiographic studies, following pulse labelling of cells with radioactive RNA precursors, it was suggested that transcription of rRNA genes takes place in the “dense fibrillar component”, and possibly also at the periphery of the “fibrillar centers” (Fakan, 1978; Thiry et al., 1985). However, using other techniques such as autoradiography with tritiated thymidine or actinomycin D, in situ-hybridization with radioactive rRNA probes and selective DNA-staining with the osmium-amine Feulgen-like reaction, DNA (including rDNA) could be detected only in the fibrillar centers (for reviews see Hernandez-Verdun, 1983; Goessens, 1984). To reconcile these seemingly contrasting results it was proposed that the fibrillar centers contain inactive rDNA in a relatively high packing density, thereby facilitating its detection, whereas the transcribed rRNA genes loop out into the surrounding dense fibrillar component (Stahl, 1982; Goessens, 1984). According to this concept the dense fibrillar component is formed by the superposition of rRNA-transcription units and newly formed rRNP material.

Ribosomal DNA-related sequences in a Y chromosomal lampbrush loop of Drosophila hydei

Abstract: Microdissection and microcloning of the Y chromosomal lampbrush loop pseudonucleolus from primary spermatocytes of Drosophila hydei allowed the isolation of copies of a 02 kb tandemly repeated DNA sequence family (dhMiP141) In situ hybridization confirmed its origin from a distal position in the long arm of the Y chromosome Transcript in situ hybridization showed that at least some of the repeat units are part of the transcripts of lampbrush loops The characterization of this DNA sequence revealed cross-homology to the β2 region of the 26 S rRNA gene, 600 bp downstream of the intervening sequence (IVS) insertion site The cloned DNA sequence, however, cannot be part of the rDNA repeats since it occurs as a 02 kb tandem repeat in the Y chromosome We therefore named the DNA sequence the “rally” (ribosomal and lampbrush loop Y chromosome) sequence The different repeat units of the 02 kb sequence display a moderate degree of divergence They are not found in the closely related species D neohydei or D eohydei, nor in D melanogaster We assume that this Y chromosomal DNA sequence is the result of a recent transposition into the Y chromosomal location, followed by an amplification event It is an important observation that the 02 kb sequence also occurs in the neighbouring lampbrush loop “threads” Since other DNA sequences are also found in both loops, the assumption of a functional relationship between both loop pairs, derived from genetic observations, is further supported

Structure of ribosomal genes of mammalian cells in situ

Abstract: The structural and functional organization of ribosomal genes was investigated in situ in human circulating lymphocytes and a human tumour cell line, TG cells Stereo-pair electron micrographs revealed that this ribosomal chromatin is not structured into nucleosomes, but composed of completely extended filaments, 2–3 nm thick Despite its homogeneous morphological structure only a small portion of ribosomal chromatin present in the dense fibrillar component is transcriptionally active This was demonstrated in TG cells by exclusive autoradiographic labelling on serial sections of the dense fibrillar component with 3H-uridine and by the distribution of RNase-gold particles in all the ribonucleoprotein (RNP) structures but not in the fibrillar centres The extended, non-nucleosomal configuration of both transcriptionally inactive and active ribosomal chromatin could be explained by the peculiar protein composition of this chromatin Staining with the acrolein-silvermethenamine technique for basic proteins indicated that all the completely extended ribosomal chromatin is devoid of histones, even after inactivation of transcription by actinomycin D Stereo-electron-microscopical visualisation of the Ag-NOR proteins revealed a thread-like structural organization of these proteins with a spatial distribution superimposable on that of the ribosomal chromatin filaments

Gametoclonal variation detected in the nuclear ribosomal DNA from doubled haploid lines of a spring wheat (Triticum aestivum L., cv. 'César').

Abstract: The organization of the nuclear ribosomal DNA from a parental line of wheat (Triticum aestivum L., cv. ‘Cesar’) and its anther-derived first cycle and second cycle doubled haploid lines has been analyzed by DNA-DNA molecular hybridization. Restricted DNA has been probed by three subclones of wheat nuclear ribosomal DNA covering the entire repeat unit. No significant difference was detected in the extent of methylation of ribosomal DNA of the doubled haploid lines with respect to the parental line. On the other hand, a variation has been found in the organization of the nontranscribed spacer region of ribosomal DNA of the first cycle doubled haploid line. This variation remains stable after a second cycle of in vitro androgenesis. However, one out of five second cycle doubled haploid lines so far tested showed an additional hybridization band present in the parental line but lacking in the first cycle doubled haploid line.

Hypervariation associated with a 12-nucleotide direct repeat and inferences on intergenomic homogenization of ribosomal RNA gene spacers based on the DNA sequence of a clone from the wheat Nor-D3 locus

Abstract: A ribosomal RNA gene (rDNA) unit from the Nor-D3 locus (D genome) of Triticum aestivum L. was cloned and the "nontranscribed spacer" (NTS) was sequenced. The DNA sequence was compared with previous...

Comparison of Physical Maps of Ribosomal DNA Repeating Units in Pythium, Phytophthora and Apodachlya

Abstract: SUMMARY: A satellite band in CsCl-bisbenzimide density gradients of Pythium diclinum DNA was found to consist of ribosomal DNA (rDNA) repeating units with a complexity of 10.3 kilobases (kb). Similar satellite bands were also obtained from a morphologically diverse selection of species from the Pythiaceae: Pythium torulosum (10.4 kb), Pythium irregulare (11.8 kb), Pythium anandrum (10.6 kb), Pythium paddicum (10.6 kb) and Phytophthora cryptogea (11.2 kb). Physical maps were constructed using seven endonuclease restriction enzymes and the maps were aligned on the basis of nine conserved restriction sites in a 6 kb region which was shown to be homologous to a DNA plasmid probe containing ribosomal genes from Neurospora crassa. A map of the rDNA region in Apodachlya pyrifera (10.1 kb), a species external to the Pythiaceae (Leptomitales), was also constructed to serve as a taxonomic reference. Percentage sequence divergence values indicated that P. diclinum and P. torulosum are closely related, but not identical. P. anandrum and P. irregulare also appeared closely related in spite of morphological differences. P. paddicum and Phytophthora cryptogea were the most outlying of the six species of Pythiaceae, but all six species formed a tight cluster when considered against A. pyrifera.