Identification of variability of ribosomal DNA spacer from Pseudomonas soil isolates

1994 ◽  
Vol 40 (7) ◽  
pp. 541-547 ◽  
Author(s):  
Santokh Gill ◽  
Julie Belles-Isles ◽  
Gerry Brown ◽  
Serge Gagné ◽  
Claude Lemieux ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Intergenic Spacer ◽  
Ribosomal Rna Genes ◽  
Peat Bog ◽  
Variable Segment ◽  
Limited Degree ◽  
Total Dna ◽  
Rna Genes

The polymerase chain reaction was used to amplify the spacer region located between the 16S and 23S ribosomal RNA genes of strains of Pseudomonas fluorescens and Pseudomonas putida isolated from peat bog, canola field, or arctic plants. Some of these amplified spacer regions were used to probe Southern blots of total DNA digests from the various strains of P. fluorescens and P. putida. Differences were observed in the patterns of hybridization of the various bacterial DNAs. The ribosomal DNA spacer region of four of the P. fluorescens strains examined, strains 64-3, 63-28, QP5, and R17-FP2, was about 515 base pairs (bp) in length, and contained the genes for tRNAIle and tRNAAla. The DNA sequences of two strains from canola, 64-3 and 63-28, differed at only two positions. The sequences of the peat bog strains QP5 and R17-FP2 were identical. However, differences were noted between the DNA sequence common to the pair of strains 64-3 and 63-28 and the corresponding common sequence for strains QP5 and R17-FP2. These differences were mainly concentrated in two DNA segments of 10 and 19 bp, respectively. A probe for the 19-bp variable segment that occurs in the ribosomal spacer of strains QP5 and R17-FP2 recognized total DNA from these two strains, but not DNA from other bacteria of different origins. These results suggest the existence of a limited degree of variability within the 16S-23S ribosomal DNA spacer region, and that this variability may be useful to the recognition of particular Pseudomonas strains from environmental samples.Key words: ribosomal RNA genes, intergenic spacer, Pseudomonas soil isolates, specific DNA probe.

Comparison of nuclear ribosomal RNA genes among Solanum species and other Solanaceae

Genome ◽  
1994 ◽  
Vol 37 (2) ◽  
pp. 271-279 ◽  
Author(s):  
N. Borisjuk ◽  
L. Borisjuk ◽  
G. Petjuch ◽  
V. Hemleben
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
New World ◽  
Intergenic Spacer ◽  
Solanum Species ◽  
Ribosomal Rna Genes ◽  
Nucleotide Sequence Analysis ◽  
World Species ◽  
Old World ◽  
Rna Genes

The organization of the nuclear-encoded 18S, 5.8S, and 25S ribosomal RNA genes (ribosomal DNA; rDNA) of 21 New World species from different sections of the genus Solanum, of two Old World Solanum species, and of representatives of other Solanaceae (Nicotiana, Atropa, Datura, Physalis, and Capsicum) was analyzed by restriction enzyme mapping using different rDNA specific hybridization probes. All Solanum species investigated exhibited rDNA repeats between 8.7 and 9.3 kb in length; the only exception was S. neorossii with a repeat length of 10.3 kb. Sequence heterogeneity was observed mostly in the intergenic spacer (IGS) region. Restriction sites for EcoRI and DraI in the spacer sequences were found to be characteristic for the New World species of the genus Solanum and for Lycopersicon esculentum. An additional XbaI site was detected in the spacer region of two nontuber-bearing species, S. brevidens and S. etuberosum (subsection Estolonifera Hawkes; series Etuberosa), as well as in the primitive tuber-bearing species of the series Pinnatisecta and Polyadenia (subsection Potatoe G.Don), thus demonstrating that these Mexican species are separated from the other tuber-bearing species but are closely linked to the nontuber-bearing Estolonifera group. Two EcoRI sites mapped at the 3′end of the 25S rRNA coding region seem to be characteristic for members of the Solanaceae; the first EcoRI site is apparently methylated in approximately 50% of the rDNA repeats. Southern hybridization with an IGS fragment of Solanum tuberosum as hybridization probe and nucleotide sequence analysis of the phylogenetically informative 3′ end of the 25S rDNA support the assumption that the New World species of the genus Solanum are closely related to Lycopersicon (tomato) in contrast with other Solanaceae investigated, Nicotiana, Atropa, Datura, Physalis, and Capsicum. Moreover, the New World potatoes and tomato appear to be more closely related to each other than potatoes and the Old World species Solanum nigrum and Solanum dulcamara.Key words: ribosomal DNA, intergenic spacer, methylation, evolutionary relationship, phylogeny.

Molecular evolution of the intergenic spacer in the nuclear ribosomal RNA genes of Cucurbitaceae

1993 ◽  
Vol 36 (2) ◽  
pp. 144-152 ◽  
Author(s):  
Klaus King ◽  
Ramon A. Torres ◽  
Ulrike Zentgraf ◽  
Vera Hemleben
Keyword(s):  
Molecular Evolution ◽  
Ribosomal Rna ◽  
Intergenic Spacer ◽  
Ribosomal Rna Genes ◽  
Rna Genes

scholarly journals Conserved arrangements of repeated DNA sequences in nontranscribed spacers of ciliate ribosomal RNA genes: evidence for molecular coevolution

1985 ◽  
Vol 13 (7) ◽  
pp. 2661-2680 ◽  
Author(s):  
Peter U. Challoner ◽  
Anthony A. Amin ◽  
Ronald E. Pearlman ◽  
Elizabeth H. Blackburn
Keyword(s):  
Ribosomal Rna ◽  
Dna Sequences ◽  
Ribosomal Rna Genes ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
Rna Genes

Species and Genus Specificity of the Intergenic Spacer (IGS) in the Ribosomal RNA Genes of Cucurbitaceae

1989 ◽  
Vol 44 (11-12) ◽  
pp. 1029-1034 ◽  
Author(s):  
R. A. Torres ◽  
U. Zentgraf ◽  
V. Hemleben
Keyword(s):  
Cucumis Sativus ◽  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
Cucumis Melo ◽  
Intergenic Spacer ◽  
Specific Pattern ◽  
Cross Hybridization ◽  
Cucumis Species ◽  
External Transcribed Spacer ◽  
Rna Genes

Abstract The use of intergenic spacer (IGS) fragments of plant ribosomal DNA (rDNA) for the differ­ entiation between genera and species is tested by cross-hybridization experiments with different IGS probes of two Cucurbitaceae, Cucurbita pepo (zucchini) and Cucumis sativus (cucum ber). Hybridization with cloned fragments of different parts of the IGS of ribosomal DNA exhibit a different degree of conservation within and between the Cucurbitaceae genera. In general, Cucur­ bita species seem to be closer related to each other than the Cucumis species. A repetitive element of the external transcribed spacer (ETS) shows a more genus-specific pattern, reacting only with the respective genera; the region preceding the ETS is conserved between the Cucurbita species but also cross-hybridizes weakly with the Cucumis species. AGC-rich element of the Cucumis sativus IGS (“Cfo-cluster”) is present in small amounts in Cucumis melo (melon) and even less represented in other genera of the Cucurbitaceae.

Complex organization of the length heterogeneous 5′ external spacer of mung bean (Vigna radiata) ribosomal DNA

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 723-733 ◽  
Author(s):  
Jutta Gerstner ◽  
Katrin Schiebel ◽  
Georg von Waldburg ◽  
Vera Hemleben
Keyword(s):  
Rna Polymerase ◽  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
Vigna Radiata ◽  
Mung Bean ◽  
Rna Polymerase I ◽  
Ribosomal Rna Genes ◽  
Enzyme Analysis ◽  
Polymerase I ◽  
Rna Genes

Restriction enzyme analysis and cloning of the 18S, 5.8S, and 25S ribosomal RNA genes (rDNA) of the mung bean (Vigna radiata = Phaseolus aureus) reveal length heterogeneity in the repeating units (10 – 11 kbp) localized within two different regions in the ribosomal spacer. The 1.5 – 2.0 kbp region flanking the 3′ end of the 25S rRNA contains various numbers (8 – 10) of tandemly arranged 180 bp subrepeats. After DNA sequencing a complex organized length heterogeneous 5′ external spacer built up of different numbers of 340 bp subrepeats, each flanked by 52 bp direct repeats, is detected and described for the first time for plant ribosomal DNA repeating units. Sequences occurring in front of and within this repeated structure (elements II – IV) can be combined with the motifs P1, P2, and P3. These exhibit a strong similarity to transcription initiation sites specific for RNA polymerase I described for other plant and animal rDNA investigated to date. Transcription products complementary to the complex repeated structures are detected by hybridization to total nuclear RNA. The 9 bp element V located in front of the first 340 bp region appears in duplicated form as a direct repeat with sequence similarity to SV40 (or RNA polymerase II) enhancer sequences.Key words: promoter, ribosomal RNA genes, RNA polymerase I, spacer organization, transcription.

scholarly journals Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans

EMBO Reports ◽  
2009 ◽  
Vol 11 (1) ◽  
pp. 52-58 ◽  
Author(s):  
Raffaella Santoro ◽  
Kerstin‐Maike Schmitz ◽  
Juan Sandoval ◽  
Ingrid Grummt
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
Ribosomal Rna Genes ◽  
Dna Repeats ◽  
In Trans ◽  
Rna Genes
Sign in / Sign up

Export Citation Format

Share Document