Nucleotide sequence of the 16S-23S spacer region in the rrnA operon from a blue-green alga, Anacystis nidulans

Tomioka, Noboru; Sugiura, Masahiro

doi:10.1007/bf00382079

Cited by 49 publications

(18 citation statements)

References 30 publications

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“…2 contains genes coding for tRNA ' and tRNA*'", as observed in several eubacteria including the cyanobacterium Synecbococcw sp. strain PCC 6301 (Tomioka & Sugiura, 1984), and in plastids (Graf etal., 1980;Ohyama etal., 1986). In six out of the eight independently sequenced clones, it shows a duplication of 29 nucleotides involving 14 nucleotides upstream of the tRNA1le and the first 15 nucleotides of the tRNA1le.…”

Section: Resultsmentioning

confidence: 99%

“…has not been determined because prohibitive amounts of pure D N A would be necessary but two, five and six copies were observed for other cyanobacteria (Nichols e t al., 1982). The first 395 nucleotides from the two copies of the ITS of S'nechococczis PCC 6301 have been sequenced independently (Williamson & Doolittle, 1983;Tomioka & Sugiura, 1984). Only four insertions and two deletions were observed, and Tomioka & Sugiura (1 984) concluded that the rm operons were highly conserved.…”

Section: Resultsmentioning

confidence: 99%

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Evolutionary affiliation of the marine nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067, derived by 16S ribosomal RNA sequence analysis

Wilmotte¹,

Neefs

Wächter

1994

Microbiology

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Evolutionary affiliation of the marine nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067, derived by 16S ribosomal RNA sequence analysis

Wilmotte¹,

Neefs

Wächter

1994

Microbiology

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“…The ITSs within each copy are identical in length and in sequence, and the two copies therefore encode the same tRNA gene(s). Similarly, the two ITS regions of Synechococcus PCC 6301 show only six differences in the 395 nucleotides (representing 72 % of the sequence and including both tRNA genes) available for comparison (Williamson & Doolittle, 1983 ;Tomioka & Sugiura, 1984).…”

Section: Two Different Its Regions (Its-l and Its-s)mentioning

confidence: 99%

“…Limited data have been obtained from the physical or genetic maps of the unicellular strains Synechococcus PCC 6301 (Tomioka et al, 1981), Synechococcus PCC 7002 (Chen & Widger, 1993) and Synechocystis PCC 6803 (Kaneko et al, 1996). Further information is available from the sequences of the 16S rRNA-23S rRNA ITS domain in members of several cyanobacterial genera that include the unicellular Synechococcus PCC 6301 (Tomioka & Sugiura, 1984), Synechocystis PCC 6803 (Kaneko et al, 1996) and 47 strains of the genus Microcystis (Otsuka et al, 1999), the filamentous (non-heterocystous) Arthrospira PCC 7345 (Nelissen et al, 1994), Spirulina PCC 6313 (Nelissen et al, 1994) and Trichodesmium NIBB 1067 , the heterocystous Nodularia BCNOD 9427 (Hayes & Barker, 1997) and a strain of uncertain generic identity, ' Mastigocladus HTF ' strain PCC 7518 (G. Van der Auwera & A. Wilmotte, personal communication). In addition, the sequence of the ITS of the photosynthetic cyanelle of Cyanophora paradoxa has been determined (Janssen et al, 1987).…”

Section: Introductionmentioning

confidence: 99%

Comparison of conserved structural and regulatory domains within divergent 16S rRNA–23S rRNA spacer sequences of cyanobacteria The GenBank accession numbers for the sequences reported in this paper are AF180968 and AF180969 for ITS-L and ITS-S, respectively.

et al. 2000

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PCR amplification of the internal transcribed spacer (ITS) between the 16SrRNA and 23S rRNA genes of the cyanobacterium Nostoc PCC 7120 gave three products. Two represented true ITS regions of different sizes, while the third was a heteroduplex. The longer spacer (ITS-L) contained 512 nucleotides and carried tRNA Ile and tRNA Ala genes, separated by a large stem-loop structure (V2) composed of short tandemly repeated repetitive sequences. Both tRNA genes, and the 5' half of the intervening stem, were absent from the shorter spacer (ITS-S), of length 283 nucleotides, which was otherwise almost completely identical to ITS-L. The two spacer regions of Nostoc PCC 7120 were aligned to published ITS sequences of cyanobacteria, the cyanelle of Cyanophora paradoxa and Escherichia coli. Although the ITS regions of cyanobacteria vary in length from 283 to 545 nucleotides and contain either both tRNA Ile and tRNA Ala genes, only the tRNA Ile gene, or neither, there is no correlation between ITS size and coding capacity for tRNAs. Putative secondary structures were determined for the deduced transcripts of the rrn operons of several cyanobacteria and were compared to that of E. coli. Highly conserved motifs important for folding and for maturation of the rRNA transcripts were identified, and regions homologous to bacterial antiterminators (box B-box A) were located. The conserved and variable regions of the cyanobacterial ITS are potential targets of PCR primers and oligonucleotide probes for detection and identification of cyanobacteria at different taxonomic levels.

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“…Both of these regions have been shown to encode tRNAs in some rRNA gene clusters. In the intergenic spacer, a glutamate tRNA or tandem isoleucinealanine tRNAs may be encoded (5,9,13,14,22,25). Some distal spacers have been shown to encode an aspartate and/or a tryptophan tRNA or a threonine tRNA (3,9,17 Southern hybridization analysis of rRNA and spacer tRNA genes.…”

mentioning

confidence: 99%

Novel tRNA gene organization in the 16S-23S intergenic spacer of the Streptococcus pneumoniae rRNA gene cluster

Bacot

Reeves

1991

J Bacteriol

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Isoleucine and alanine tRNAs are encoded tandemly within the 16S-23S intergenic spacer of some eubacterial rRNA gene clusters. Southern hybridization analysis and DNA sequence analysis demonstrated a novel gene organization for an rRNA gene cluster on the Streptococcus pneumoniae chromosome. A sequence specifying an alanine tRNA was found within the intergenic spacer, but no sequence specifying an isoleucine tRNA was found there. Southern hybridization analysis indicated that the location of the isoleucine tRNA gene was near the 5S rRNA gene in two of four rRNA gene clusters.Typically, the gene organization of eubacterial rRNA gene clusters is 5'-16S-23S-5S-3' (2 and references within; 20), although several exceptions have been observed (12,21,23 Southern hybridization analysis of rRNA and spacer tRNA genes. Total DNA was extracted (11) and purified from late-log-phase cultures of S. pneumoniae (ATCC 33400). The concentration of the DNA preparation was determined by the diphenylamine assay as previously described (6). In separate reactions, 1 ,ug of total DNA was digested with either HindlIl or PstI. Conditions for the digestions were those specified by the supplier of the restriction endonucleases (Bethesda Research Laboratories, Inc., Gaithersburg, Md.). The restriction digests and lambda HindIll fragments were electrophoresed in a 1% agarose gel. The fractionated DNA was transferred to a solid support membrane (Nytran; Schleicher & Schuell, Inc., Keene, N.H.) as previously described (19). The membrane-bound DNA fragments were sequentially probed with 5'-end-labeled [y-32P] ATP oligodeoxyribonucleotides specific for the three rRNA genes and the tRNAIle and tRNAAla genes. Probes are described in Table 1. The 5S rDNA probe was mixed, in that the sixth nucleotide was synthesized with equimolar ratios of all four deoxyribonucleotides, because of the variability at that position in eubacterial 5S rRNAs. Conditions for prehybridizations, hybridizations, and probe removal were those specified by the supplier of the hybridization membrane (Schleicher & Schuell). Figure 1 shows the results of the hybridization experiments. Estimated sizes of the DNA fragments that hybridized with the probes are presented in Most striking of our observations was the lack of similarity between the hybridization patterns generated from the tDNAIIe and tDNAAla probes. Two signals corresponding to 6.1 and 3.5 kb in the HindIII-digested DNA were observed from the hybridization with the tDNAI'e probe. Four signals corresponding to 6.1, 3.5, 3.2, and 2.5 kb were observed when the 5S rDNA probe was hybridized against the HindIII-digested DNA. Two signals corresponding to 8.9 and 7.1 kb in the PstI-digested DNA were observed from the hybridization with the tDNAIle probe. Four signals corresponding to 20.0, 8.9, 7.8, and 7.1 kb were observed following hybridization of the 5S rDNA probe to PstI-digested DNA. Thus, the two signals from the tDNAIle hybridization correspond to two of the four signals from the 5S rDNA hybridization (HindlIl-or PstI-di...

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Nucleotide sequence of the 16S-23S spacer region in the rrnA operon from a blue-green alga, Anacystis nidulans

Cited by 49 publications

References 30 publications

Evolutionary affiliation of the marine nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067, derived by 16S ribosomal RNA sequence analysis

Evolutionary affiliation of the marine nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067, derived by 16S ribosomal RNA sequence analysis

Comparison of conserved structural and regulatory domains within divergent 16S rRNA–23S rRNA spacer sequences of cyanobacteria The GenBank accession numbers for the sequences reported in this paper are AF180968 and AF180969 for ITS-L and ITS-S, respectively.

Novel tRNA gene organization in the 16S-23S intergenic spacer of the Streptococcus pneumoniae rRNA gene cluster

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