Organization of the ribosomal RNA genes in Mycoplasma hyopneumoniae: The 5S rRNA gene is separated from the 16S and 23S rRNA genes

The analyses of previously described 5S rRNA gene sequences show that some of the expressed 5S rRNA genes present in the mouse and rat genomes were derived from the retrotransposition of 5S rRNA transcripts. These analyses demonstrate that new 5S rRNA gene copies can originate by retrotransposition and that some of these retrotranscribed genes are expressed. Key words: 5S ribosomal RNA genes, retrotransposition, retroposons.

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Basonuclin is associated with the ribosomal RNA genes on human keratinocyte mitotic chromosomes

Journal of Cell Science ◽

10.1242/jcs.112.18.3039 ◽

1999 ◽

Vol 112 (18) ◽

pp. 3039-3047 ◽

Cited By ~ 2

Author(s):

H. Tseng ◽

J.A. Biegel ◽

R.S. Brown

Keyword(s):

Ribosomal Rna ◽

Zinc Fingers ◽

Hair Follicles ◽

Ribosomal Rna Genes ◽

Rrna Genes ◽

Control Element ◽

Rrna Gene ◽

Metaphase Chromosomes ◽

Acrocentric Chromosomes ◽

Rna Genes

Basonuclin is a zinc finger protein mainly expressed in keratinocytes of the basal layer of epidermis and the outer root sheath of hair follicles. It is also found in abundance in the germ cells of testis and ovary. In cultured keratinocytes, basonuclin is associated with chromatin in all phases of the cell cycle, including mitosis. By immunocytochemical methods, we demonstrate here that in mitosis basonuclin is associated with the short arms of the acrocentric chromosomes and with other loci on many metaphase chromosomes of human keratinocytes. Using the evolutionarily highly conserved N-terminal pair of zinc fingers in an electrophoresis mobility shift assay, we demonstrate that the DNA target sequences of basonuclin on the acrocentric chromosomes are likely to be within the promoter region of the 45S rRNA gene transcription unit. DNase I footprinting shows that basonuclin zinc fingers interact with the upstream control element of this promoter, which is necessary for the high level of transcription of the rRNA genes. This result suggests that basonuclin may be a tissue-specific transcription factor for the ribosomal RNA genes.

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Molecular characterization and chromosomal mapping of the 5S rRNA gene in Solea senegalensis: a new linkage to the U1, U2, and U5 small nuclear RNA genes

Genome ◽

10.1139/g05-068 ◽

2006 ◽

Vol 49 (1) ◽

pp. 79-86 ◽

Cited By ~ 41

Author(s):

Manuel Manchado ◽

Eugenia Zuasti ◽

Ismael Cross ◽

Alejandro Merlo ◽

Carlos Infante ◽

...

Keyword(s):

5S Rdna ◽

5S Rrna ◽

Rrna Genes ◽

Solea Senegalensis ◽

Rrna Gene ◽

Small Nuclear Rna ◽

5S Rrna Gene ◽

Nuclear Rna ◽

Pcr Products ◽

Rna Genes

Some units of the 5S rDNA of Solea senegalensis were amplified by PCR and sequenced. Three main PCR products (227, 441, and 2166 bp) were identified. The 227- and 441-bp fragments were characterized by highly divergent nontranscribed spacer sequences (referred to as NTS-I and NTS-II) that were 109 and 324 bp long, respectively, yet their coding sequences were nearly identical. The 2166-bp 5S rDNA unit was composed of two 5S rRNA genes separated by NTS-I and followed by a 1721-bp spacer containing the U2, U5, and U1 small nuclear RNA genes (snRNAs). They were inverted and arranged in the transcriptional direction opposite that of the 5S rRNA gene. This simultaneous linkage of 3 different snRNAs had never been observed before. The PCR products were used as probes in fluorescence in situ hybridization experiments to locate the corresponding loci on the chromosomes of S. senegalensis. A major 5S rDNA chromosomal site was located along most of the short arm of a submetacentric pair, while a minor site was detected near the centromeric region of an acrocentric pair.Key words: soleidae, pleuronectiformes, 5S rDNA, Solea, snRNAs linkage.

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Comparison of the 23S ribosomal RNA genes and the spacer region between the 16S and 23S rRNA genes of the closely related Mycobacterium avium and Mycobacterium paratuberculosis and the fast-growing Mycobacterium phlei

Microbiology ◽

10.1099/13500872-140-5-1103 ◽

1994 ◽

Vol 140 (5) ◽

pp. 1103-1108 ◽

Cited By ~ 19

Author(s):

J. W. B. van der Giessen ◽

R. M. Haring ◽

B. A. M. van der Zeijst

Keyword(s):

Mycobacterium Avium ◽

Ribosomal Rna ◽

Rrna Genes ◽

23S Rrna ◽

Mycobacterium Paratuberculosis ◽

Fast Growing ◽

Mycobacterium Phlei ◽

23S Rrna Genes ◽

23S Ribosomal Rna ◽

Rna Genes

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The 18S and 5S ribosomal RNA genes in Oenothera mitochondria: Sequence rearrangments in the 18S and 5S rRNA genes of higher plants

MGG Molecular & General Genetics ◽

10.1007/bf00332930 ◽

1985 ◽

Vol 198 (3) ◽

pp. 404-410 ◽

Cited By ~ 43

Author(s):

Axel Brennicke ◽

Sabine Möller ◽

Paul A. Blanz

Keyword(s):

Ribosomal Rna ◽

Higher Plants ◽

Ribosomal Rna Genes ◽

5S Rrna ◽

Rrna Genes ◽

5S Ribosomal Rna ◽

5S Rrna Genes ◽

Rna Genes

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Construction of the physical maps of Mycoplasma hyopneumoniae and Mycoplasma flocculare and the location of rRNA genes on these maps

Canadian Journal of Microbiology ◽

10.1139/m92-107 ◽

1992 ◽

Vol 38 (7) ◽

pp. 659-663 ◽

Cited By ~ 7

Author(s):

Y. Huang ◽

G. W. Stemke

Keyword(s):

Mycoplasma Hyopneumoniae ◽

Cross Reactivity ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Physical Maps ◽

Close Relationship ◽

23S Rrna Genes ◽

Mycoplasma Flocculare ◽

Porcine Respiratory

The genomes of Mycoplasma flocculare and Mycoplasma hyopneumoniae, two mycoplasmas of the porcine respiratory system, were studied. Based upon antigenic cross-reactivity and DNA–DNA hybridization, these species have given indication of a close genetic relationship. By using field-inversion gel electrophoresis and employing the restriction digest fragments obtained from the gels as the probes, physical maps of the genomes of the two species were constructed. Mycoplasma hyopneumoniae is similar to M. flocculare in having a single set of rRNA genes and the 5S-rRNA gene is separated from the 16S and 23S rRNA genes. Based upon the location of the rRNA genes on the physical maps in both species, the distance between the 5S and the 16S and 23S rRNA genes is at least 150 kbp. Thus, there is further evidence for the close relationship between these organisms. Key words: Mycoplasma, Mollicutes, physical maps, rRNA.

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Cloning and Sequence Analysis of 5S Ribosomal RNA Gene(s) and Associated Intergenic Spacer Regions in Carica Species

International Journal of Biology ◽

10.5539/ijb.v13n1p1 ◽

2021 ◽

Vol 13 (1) ◽

pp. 1

Author(s):

Mahipal Singh ◽

Pushpa Yadav ◽

Anand K. Yadav

Keyword(s):

Sequence Analysis ◽

Ribosomal Rna ◽

Carica Papaya ◽

Intergenic Spacer ◽

5S Rrna ◽

Rrna Genes ◽

Rrna Gene ◽

Ribosomal Rna Gene ◽

5S Ribosomal Rna ◽

5S Rrna Gene

The 5S ribosomal RNA gene(s) and their associated intergenic spacer regions were amplified from Carica papaya and Carica quercifolia by polymerase chain reaction. Both Carica species exhibited differently sized amplification products. Sequence analysis of these PCR products revealed that the 5S rRNA genes are arranged as tandem repeats in these regions. Sequence data revealed that the 5S rRNA gene from Carica quercifolia was 119 bp in length. Sequence variation was observed in various 5S rRNA gene copies cloned from Carica quercifolia. Only truncated 5S rRNA gene but with its full spacer region was recovered from Carica papaya. Interestingly, intergenic spacer sequence cloned from Carica papaya contained two specific domains, a 30bp “CT” rich domain exhibiting 95-100% homology to several human chromosomes and a domain matching with mitrocomin precursor, a photo-protein from Mitrocoma cellularia. The role of 5S rRNA gene and their spacer regions in discerning the germplasm and in adaptation of the species is discussed.

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A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication

Molecular and Cellular Biology ◽

10.1128/mcb.9.10.4416-4421.1989 ◽

1989 ◽

Vol 9 (10) ◽

pp. 4416-4421

Author(s):

W S Grayburn ◽

E U Selker

Keyword(s):

Dna Methylation ◽

Tandem Duplication ◽

De Novo ◽

5S Rrna ◽

Rrna Genes ◽

Structural Basis ◽

Rrna Gene ◽

Oak Ridge ◽

5S Rrna Gene ◽

5S Rrna Genes

5S rRNA genes of Neurospora crassa are generally dispersed in the genome and are unmethylated. The xi-eta region of Oak Ridge strains represents an informative exception. Most of the cytosines in this region, which consists of a diverged tandem duplication of a 0.8-kilobase-pair segment including a 5S rRNA gene, appear to be methylated (E. U. Selker and J. N. Stevens, Proc. Natl. Acad. Sci. USA 82:8114-8118, 1985). Previous work demonstrated that the xi-eta region functions as a portable signal for de novo DNA methylation (E. U. Selker and J. N. Stevens, Mol. Cell. Biol. 7:1032-1038, 1987; E. U. Selker, B. C. Jensen, and G. A. Richardson, Science 238:48-53, 1987). To identify the structural basis of this property, we have isolated and characterized an unmethylated allele of the xi-eta region from N. crassa Abbott 4. The Abbott 4 allele includes a single 5S rRNA gene, theta, which is different from all previously identified Neurospora 5S rRNA genes. Sequence analysis suggests that the xi-eta region arose from the theta region by duplication of a 794-base-pair segment followed by 267 G.C to A.T mutations in the duplicated DNA. The distribution of these mutations is not random. We propose that the RIP process of N. crassa (E. U. Selker, E. B. Cambareri, B. C. Jensen, and K. R. Haack, Cell 51:741-752, 1987; E. U. Selker, and P. W. Garrett, Proc. Natl. Acad. Sci. USA 85:6870-6874, 1988; E. B. Cambareri, B. C. Jensen, E. Schabtach, and E. U. Selker, Science 244:1571-1575, 1989) is responsible for the numerous transition mutations and DNA methylation in the xi-eta region. A long homopurine-homopyrimidine stretch immediately following the duplicated segment is 9 base pairs longer in the Oak Ridge allele than in the Abbott 4 allele. Triplex DNA, known to occur in homopurine-homopyrimidine sequences, may have mediated the tandem duplication.

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Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

10.21203/rs.3.rs-24857/v3 ◽

2020 ◽

Author(s):

Abigail Hui En Chan ◽

Kittipong Chaisiri ◽

Serge Morand ◽

Naowarat Saralamba ◽

Urusa Thaenkham

Keyword(s):

Genetic Marker ◽

Genetic Markers ◽

Molecular Systematics ◽

Ribosomal Rna ◽

Ribosomal Rna Genes ◽

16S Ribosomal Rna ◽

12S Rrna ◽

Rrna Gene ◽

12S Rrna Gene ◽

Rna Genes

Abstract Background Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics. Methods To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms. Results The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers. Conclusions This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

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Spontaneous Erythromycin Resistance Mutation in a 23S rRNA Gene, rrlA, of the Extreme Thermophile Thermus thermophilus IB-21

Journal of Bacteriology ◽

10.1128/jb.183.14.4382-4385.2001 ◽

2001 ◽

Vol 183 (14) ◽

pp. 4382-4385 ◽

Cited By ~ 9

Author(s):

Steven T. Gregory ◽

Jamie H. D. Cate ◽

Albert E. Dahlberg

Keyword(s):

Genetic Manipulation ◽

Thermus Thermophilus ◽

Resistance Mutation ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Erythromycin Resistance ◽

23S Rrna Gene ◽

Resistant Mutants ◽

23S Rrna Genes

ABSTRACT Spontaneous, erythromycin-resistant mutants of Thermus thermophilus IB-21 were isolated and found to carry the mutation A2058G in one of two 23S rRNA operons. The heterozygosity of these mutants indicates that A2058G confers a dominant or codominant phenotype in this organism. This mutation provides a valuable tool for the genetic manipulation of the 23S rRNA genes ofThermus.

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