scholarly journals 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

1987 ◽  
Vol 246 (2) ◽  
pp. 519-527 ◽  
Author(s):  
B E H Maden ◽  
C L Dent ◽  
T E Farrell ◽  
J Garde ◽  
F S McCallum ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Single Point ◽  
Transcription Unit ◽  
Internal Transcribed Spacers ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Evolutionary Divergence ◽  
Length Variation ◽  
External Transcribed Spacer ◽  
Ribosomal Transcription Unit

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.

Initiation and termination of DNA replication in human rRNA genes

1993 ◽  
Vol 13 (10) ◽  
pp. 6600-6613
Author(s):  
R D Little ◽  
T H Platt ◽  
C L Schildkraut
Keyword(s):  
Dna Replication ◽  
Ribosomal Dna ◽  
Regulatory Elements ◽  
Transcription Unit ◽  
Replication Initiation ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Replication Forks ◽  
Nontranscribed Spacer ◽  
Dna Repeat

We have used the multicopy human rRNA genes as a model system to study replication initiation and termination in mammalian chromosomes. Enrichment for replicating molecules was achieved by isolating S-phase enriched populations of cells by centrifugal elutriation, purification of DNA associated with the nuclear matrix, and a chromatographic procedure that enriches for molecules containing single-stranded regions, a characteristic of replication forks. Two-dimensional agarose gel electrophoresis techniques were used to demonstrate that replication appears to initiate at multiple sites throughout most of the 31-kb nontranscribed spacer (NTS) of human ribosomal DNA but not within the 13-kb transcription unit or adjacent regulatory elements. Although initiation events were detected throughout the majority of the NTS, some regions may initiate more frequently than others. Termination of replication, the convergence of opposing replication forks, was found throughout the ribosomal DNA repeat units, and, in some repeats, specifically at the junction of the 3' end of the transcription unit and the NTS. This site-specific termination of replication is the result of pausing of replication forks near the sites of transcription termination. The naturally occurring multicopy rRNA gene family offers a unique system to study mammalian DNA replication without the use of chemical synchronization agents.

Structure and molecular evolution of the ribosomal DNA external transcribed spacer in the cockroach genus Blattella

Genome ◽  
2011 ◽  
Vol 54 (3) ◽  
pp. 222-234 ◽  
Author(s):  
Dmitry V. Mukha ◽  
Vera Mysina ◽  
Valeria Mavropulo ◽  
Coby Schal
Keyword(s):  
Ribosomal Dna ◽  
Multigene Family ◽  
Internal Transcribed Spacers ◽  
Rrna Genes ◽  
Nucleotide Substitutions ◽  
Rdna Cluster ◽  
Nontranscribed Spacer ◽  
External Transcribed Spacer ◽  
A New Species ◽  
Nucleolus Organizers

The ribosomal DNA (rDNA) cluster of insects contains several hundred repeating structural–functional units and, therefore, is a typical example of a multigene family. Eukaryotic ribosomal RNA (rRNA) genes (18S, 5.8S, and 28S like) are arranged in tandemly repeated clusters in the nucleolus organizers, separated by several spacers, namely the nontranscribed spacer, the external transcribed spacer (ETS), and the internal transcribed spacers. The nucleotide sequences of the ETS of the three closely related Blattella cockroach species, Blattella germanica (Linnaeus, 1767), Blattella asahinai (Mizukubo, 1981), and Blattella lituricollis (Walker, 1868), were determined and compared. The three species had relatively similar ETS lengths, and sequence differences among them could be explained by two types of rearrangements, namely deletions of subrepeats and nucleotide substitutions. Minor ETS variants in B. germanica differed from the major variant in the same way that the major ETS variants of the three Blattella species differed from each other. Concerted evolution and the birth-and-death models, which are often invoked to explain the diversity and evolution of the multigene families of rDNA clusters, are discussed in the light of our data. A new model is proposed to explain the evolutionary reorganization of the ETS region: evolution of rDNA by “magnification-and-fixation” is characterized by magnification of minor subrepeats, which become adaptive in a new rapidly changed environment, and subsequent fixation of this variant type as a major component of the multigene family of a new species.

scholarly journals Initiation and termination of DNA replication in human rRNA genes.

1993 ◽  
Vol 13 (10) ◽  
pp. 6600-6613 ◽  
Author(s):  
R D Little ◽  
T H Platt ◽  
C L Schildkraut
Keyword(s):  
Dna Replication ◽  
Ribosomal Dna ◽  
Regulatory Elements ◽  
Transcription Unit ◽  
Replication Initiation ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Replication Forks ◽  
Nontranscribed Spacer ◽  
Dna Repeat

We have used the multicopy human rRNA genes as a model system to study replication initiation and termination in mammalian chromosomes. Enrichment for replicating molecules was achieved by isolating S-phase enriched populations of cells by centrifugal elutriation, purification of DNA associated with the nuclear matrix, and a chromatographic procedure that enriches for molecules containing single-stranded regions, a characteristic of replication forks. Two-dimensional agarose gel electrophoresis techniques were used to demonstrate that replication appears to initiate at multiple sites throughout most of the 31-kb nontranscribed spacer (NTS) of human ribosomal DNA but not within the 13-kb transcription unit or adjacent regulatory elements. Although initiation events were detected throughout the majority of the NTS, some regions may initiate more frequently than others. Termination of replication, the convergence of opposing replication forks, was found throughout the ribosomal DNA repeat units, and, in some repeats, specifically at the junction of the 3' end of the transcription unit and the NTS. This site-specific termination of replication is the result of pausing of replication forks near the sites of transcription termination. The naturally occurring multicopy rRNA gene family offers a unique system to study mammalian DNA replication without the use of chemical synchronization agents.

scholarly journals Trichosporon xylopini sp. nov., a hemicellulose-degrading yeast isolated from the wood-inhabiting beetle Xylopinus saperdioides

2011 ◽  
Vol 61 (10) ◽  
pp. 2538-2542 ◽  
Author(s):  
Pushpa Gujjari ◽  
Sung-Oui Suh ◽  
Ching-Fu Lee ◽  
Jianlong J. Zhou
Keyword(s):  
Type Strain ◽  
Sole Carbon Source ◽  
Novel Species ◽  
Internal Transcribed Spacers ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Yeast Strains ◽  
Lsu Rrna Gene ◽  
Coleoptera Tenebrionidae

Four arthroconidium-producing yeasts were isolated from the gut of wood-inhabiting tenebrionid and passalid beetles. The rRNA genes of these yeast strains were sequenced, compared and analysed. The sequence results and other taxonomic characterizations placed two of the strains into Trichosporon porosum, and the remaining strains, EH024T and EH026 which were isolated from Xylopinus saperdioides (Coleoptera: Tenebrionidae), into a novel species of the genus Trichosporon in the Porosum clade. Strain EN6S23 was independently isolated from forest soil in Taiwan and was identified as the same novel species based on identical sequences in the internal transcribed spacers (ITS) and the D1/D2 region of the LSU rRNA gene and similar physiological characteristics to those of strains EH024T and EH026. The three strains can assimilate cellulose and xylan as sole carbon source, and are clearly distinguished from their closest taxon, T. porosum, by 14 nt differences in the ITS and D1/D2 region. These strains did not reproduce sexually under the laboratory conditions tested. The novel species is proposed as Trichosporon xylopini sp. nov. (type strain EH024T  = ATCC MYA-4670T  = CBS 11841T).

Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae)

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 595-604 ◽  
Author(s):  
Ana Insua ◽  
María J López-Piñón ◽  
Ruth Freire ◽  
Josefina Méndez
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Aequipecten Opercularis

The internal transcribed spacer (ITS) region of the ribosomal DNA from the European scallops Aequipecten opercularis, Mimachlamys varia, Hinnites distortus, and Pecten maximus was PCR amplified and sequenced. For each species, three or five clones were examined. The size ranged between 636 and 713 bp (ITS1, 209–276 bp; 5.8S rRNA gene, 157 bp; ITS2, 270–294 bp) and GC content ranged between 47 and 50% (ITS1, 43–49%; 5.8S rRNA gene, 56–57%; ITS2, 44–49%). Variation within repeats was minimal; only clones from M. varia and P. maximus displayed a few variable sites in ITS2. Among scallops, including Chlamys farreri whose ITS sequence appears in databases, significant variation was observed in both ITS1 and ITS2. Phylogenetic analysis using ITS1, ITS2, or both spacer sequences always yielded trees with similar topology. Aequipecten opercularis and P. maximus grouped in one clade and the other three scallops (C. farreri, M. varia, and H. distortus) in another, where M. varia and H. distortus are the more closely related species. These results provide new insights into the evolutionary relationships of scallop species and corroborate the close evolutionary relationship between the tribes Aequipectinini and Pectinini previously deduced from 18S rDNA sequences.Key words: scallops, Pectinidae, ribosomal DNA, internal transcribed spacers, phylogeny.

scholarly journals Evidence that intergenic spacer repeats of Drosophila melanogaster rRNA genes function as X-Y pairing sites in male meiosis, and a general model for achiasmatic pairing.

Genetics ◽  
1992 ◽  
Vol 132 (2) ◽  
pp. 529-544 ◽  
Author(s):  
B D McKee ◽  
L Habera ◽  
J A Vrana
Keyword(s):  
Drosophila Melanogaster ◽  
Topoisomerase I ◽  
Meiotic Chromosome ◽  
Intergenic Spacer ◽  
Transcription Unit ◽  
P Element ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Meiotic Pairing ◽  
Rrna Transcription

Abstract In Drosophila melanogaster males, X-Y meiotic chromosome pairing is mediated by the nucleolus organizers (NOs) which are located in the X heterochromatin (Xh) and near the Y centromere. Deficiencies for Xh disrupt X-Y meiotic pairing and cause high frequencies of X-Y nondisjunction. Insertion of cloned rRNA genes on an Xh- chromosome partially restores normal X-Y pairing and disjunction. To map the sequences within an inserted, X-linked rRNA gene responsible for stimulating X-Y pairing, partial deletions were generated by P element-mediated destabilization of the insert. Complete deletions of the rRNA transcription unit did not interfere with the ability to stimulate X-Y pairing as long as most of the intergenic spacer (IGS) remained. Within groups of deletions that lacked the entire transcription unit and differed only in length of residual IGS material, pairing ability was proportional to the dose of 240-bp intergenic spacer repeats. Deletions of the complete rRNA transcription unit or the 28S sequences alone blocked nucleolus formation, as determined by binding of an antinucleolar antibody, yet did not interfere with pairing ability, suggesting that X-Y pairing may not be mechanistically related to nucleolus formation. A model for achiasmatic pairing in Drosophila males based upon the combined action of topoisomerase I and a strand transferase is proposed.

scholarly journals Kinetic Bias in Estimates of Coastal Picoplankton Community Structure Obtained by Measurements of Small-Subunit rRNA Gene PCR Amplicon Length Heterogeneity

1998 ◽  
Vol 64 (11) ◽  
pp. 4522-4529 ◽  
Author(s):  
Marcelino Suzuki ◽  
Michael S. Rappé ◽  
Stephen J. Giovannoni
Keyword(s):  
Clone Library ◽  
Fluorescence Emission ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Length Variation ◽  
Small Subunit Rrna ◽  
Gene Frequencies ◽  
Rdna Sequences

ABSTRACT Marine bacterioplankton diversity was examined by quantifying natural length variation in the 5′ domain of small-subunit (SSU) rRNA genes (rDNA) amplified by PCR from a DNA sample from the Oregon coast. This new technique, length heterogeneity analysis by PCR (LH-PCR), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. Relationships between the sizes of amplicons and gene phylogeny were predicted by an analysis of 366 SSU rDNA sequences from cultivated marine bacteria and from bacterial genes cloned directly from environmental samples. LH-PCR was used to compare the distribution of bacterioplankton SSU rDNAs from a coastal water sample with that of an SSU rDNA clone library prepared from the same sample and also to examine the distribution of genes in the PCR products from which the clone library was prepared. The analysis revealed that the relative frequencies of genes amplified from natural communities are highly reproducible for replicate sets of PCRs but that a bias possibly caused by the reannealing kinetics of product molecules can skew gene frequencies when PCR product concentrations exceed threshold values.

Phylogeny of Sisymbrium (Brassicaceae) based on ITS sequences of nuclear ribosomal DNA

2002 ◽  
Vol 80 (9) ◽  
pp. 1002-1017 ◽  
Author(s):  
Suzanne I Warwick ◽  
Ihsan A Al-Shehbaz ◽  
Robert A Price ◽  
Connie Sauder
Keyword(s):  
Ribosomal Dna ◽  
New World ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Old World ◽  
5.8S Rrna Gene

The genus Sisymbrium as currently circumscribed includes about 94 species disjunctly distributed in the Old (41 spp.) and the New World (53 spp.). Sisymbrium has been variously delimited, with several segregate genera proposed (subtribe Sisymbriinae) primarily for the new World taxa, including Schoenocrambe, Coelophragmus, and Mostacillastrum. Using sequence data from the internal transcribed spacers of nuclear ribosomal DNA and the 5.8S rRNA gene (collectively, ITS region), we examined the evolutionary relationships of Old and New World Sisymbrium species with its segregate genera and the validity of O.E. Schulz's classical sectional treatment of Sisymbrium. Sequence data were obtained from 33 Sisymbrium species, representing all 14 sections and two Sisymbrium species formerly assigned to segregate genera Coelophragmus and Mostacillastrum (subtribe Sisymbriinae), and two putative Sisymbrium species currently assigned to Neotorularia. Sequence data were also obtained from 26 taxa from segregate or related genera includingSchoenocrambe, Werdermannia (subtribe Sisymbriinae), eight genera in the Thelypodieae, Sibara (tribe Arabideae) and Pringlea (tribe Pringleeae), four members of the tribe Brassiceae, and three other Neotorularia species. Results from maximum parsimony analysis showed a polyphyletic origin for Sisymbrium and did not correspond well to Schulz's sectional classification. Sisymbrium species were split into three major clades: Old World Sisymbrium (including Neotorularia aculeolata, Neotorularia afghanica, and the type species of Schoenocrambe, Schoenocrambe linifolia, the sole New World member of this Old World clade); New World Sisymbrium (along with the remaining New World taxa) and designated as the New World Thelypodieae alliance; and the tribe Brassiceae ( including Sisymbrium supinum and Sisymbrium thellungii).Key words: Sisymbrium, Schoenocrambe, ITS, Thelypodieae, taxonomy, Brassicaceae.

Sequence Length Variation of Internal Genic Space of 16S rDNA-23S rDNA in Bacterium with High Yield of Hydrogen Production

2011 ◽  
Vol 183-185 ◽  
pp. 1413-1416
Author(s):  
Yong Feng Li ◽  
Yi Xuan Wang ◽  
Lu Wang ◽  
Zhan Qing Wang
Keyword(s):  
16S Rdna ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
High Yield ◽  
23S Rrna ◽  
Sequence Length ◽  
Rrna Gene ◽  
Length Variation ◽  
Intergenic Spacer Region

To develop the identification of species for fermentative biohydrogen-producing bacterium, scholars have found a method which is based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions. In the study, a large fragment of the rDNA operon, including the 16S rDNA, the intergenic spacer region (ISR) and approximately 2000 bases of the 23S rDNA, were polymerasechain reaction (PCR) amplified. The PCR amplification of the genomic DNA of Leptonema ilk strain 3055 using primers directed against conserved regions of the rRNA operon provided evidence that the 16S and 23S rRNA genes were linked via an intergenic spacer region. The sequencing of the intergenic spacer region indicated that it was 435 nucleotides in length and sequence similarity searches revealed that it bore no homology to any known sequences including tRNA available in databases.

scholarly journals Bacterial Primary Colonization and Early Succession on Surfaces in Marine Waters as Determined by Amplified rRNA Gene Restriction Analysis and Sequence Analysis of 16S rRNA Genes

2000 ◽  
Vol 66 (2) ◽  
pp. 467-475 ◽  
Author(s):  
Hongyue Dang ◽  
Charles R. Lovell
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Restriction Analysis ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Marine Waters ◽  
Early Stages ◽  
Early Succession

ABSTRACT The nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. However, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. Experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tidal creek for 24 or 72 h. The organisms colonizing these surfaces were examined by using a cultivation-independent approach, amplified ribosomal DNA restriction analysis. The goals of this study were to assess the diversity of bacterial colonists involved in early succession on a variety of surfaces and to determine the phylogenetic affiliations of the most common early colonists. Substantial differences in the representation of different cloned ribosomal DNA sequences were found when the 24- and 72-h incubations were compared, indicating that some new organisms were recruited and some other organisms were lost. Phylogenetic analyses of the most common sequences recovered showed that the colonists were related to organisms known to inhabit surfaces or particles in marine systems. A total of 22 of the 26 clones sequenced were affiliated with theRoseobacter subgroup of the α subdivision of the divisionProteobacteria (α-Proteobacteria), and most of these clones were recovered at a high frequency from all surfaces after 24 or 72 h of incubation. Two clones were affiliated with the Alteromonas group of the γ-Proteobacteriaand appeared to be involved only in the very early stages of colonization (within the first 24 h). A comparison of the colonization patterns on the test surfaces indicated that the early bacterial community succession rate and/or direction may be influenced by surface physicochemical properties. However, organisms belonging to the Roseobacter subgroup are ubiquitous and rapid colonizers of surfaces in coastal environments.

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