Compilation of small ribosomal sobunit RNA sequences

Huysmans, Erik; Wächter, Rupert De

doi:10.1093/nar/14.suppl.r73

Cited by 76 publications

(48 citation statements)

References 17 publications

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“…Although the conservation of rRNA sequehce is a probable cause of the apparent homology, examination of 60 small-subunit rRNA sequences from diverse organisms indicates that sequences specifying ORF16 are highly conserved in the eubacteria and plant organelles (2,17,20,34) (Table 3). This is especially true of the region containing the SD sequence and the GTG -2 and ATG +1 start codons.…”

Section: Discussionmentioning

confidence: 99%

In vivo translation of a region within the rrnB 16S rRNA gene of Escherichia coli

Berg¹,

Squires²

1987

J Bacteriol

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In this study we show that a segment of the Escherichia coli rrnB 16S gene can be translated in vivo. Other laboratories have previously reported that there are internal transcription and translation signals and open reading frames within the E. coli rrnB rRNA operon. Their studies revealed a translation start signal followed by a 252-base-pair open reading frame (ORF16) within the 16S gene and detected a promoter (P16) in the same general region by using in vitro RNA polymerase binding and transcription initiation assays. By using plasmid gene fusions of ORF16 to lacZ we showed that an ORF16'-'2-galactosidase fusion protein was made in vivo.Transcripts encoding the fusion protein were expressed either from the rrnB PIP2 control region or from a hybrid trp-lac promoter (tacP), but the amount of expression was considerably less than for a lacZ control plasmid. We used fusions to the cat gene to show that P16 is one-half as active as lacP. Deletions were used to show that P16 is located within ORF16 and thus cannot promote a transcript encoding the ORF16 peptide. A comparison of sequences from different organisms shows that ORF16 and P16 lie in a highly conserved region of the procaryotic 16S RNA structure. The first 20 amino acids of 0RF16 are conserved in most eubacterial and plant organellar sequences, and promoter activity has been detected in this region of the Caulobacter crescentus sequence by other workers.The possibility that rRNA codes for an amino acid sequence has been considered by many workers. Both transcriptional and translational start signals and open reading frames within rRNA genes have been described previously. However, evidence for the translation of rRNA has never been reported, and it is generally believed that the extensive secondary structure and protein interactions of rRNA molecules render them inaccessible to the translational machinery. In this study we show that a prominent open reading frame near the end of the Escherichia coli rrnB 16S gene could be translated in vivo.The E. coli genome contains seven rRNA operons, each with genes coding for 16S, 23S, and 5S rRNA subunits, as well as a variable number of tRNAs. The rrnB (Fig. 1) operon is located at 89 min on the E. coli genetic map. Transcription of rrn operons initiates from a control region that contains tandem promoters (PP2) (11,44) and an antitermination (AT) system, presumably to protect the extensive untranslated transcript from premature termination by the Rho-specific termination system of the cell (22). The polycistronic transcript is subsequently processed into mature 16S, 23S, and 5S rRNAs and tRNAs. The rrnB operon has been sequenced in its entirety (7, 8); rRNA sequencing (9) as well as partial DNA sequences from other operons (11,15,33,35,(42)(43)(44) (Fig. 2). In vitro transcription initiation has been noted from the same general region of the rrnB 16S gene of E. coli (39) and the * Corresponding author.homologous region within the 16S gene of Caulobacter crescentus (2).In this paper we used ORF16'-'lacZ gene fusi...

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Section: Discussionmentioning

confidence: 99%

In vivo translation of a region within the rrnB 16S rRNA gene of Escherichia coli

Berg¹,

Squires²

1987

J Bacteriol

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“…Sequences were aligned with previously entered sequences, including previously published sequences from the following eubacteria: Agrobacterium tumefaciens, Pseudomonas testosteroni, E. coli, Proteus vulgaris, Bacillus subtilis, Heliobacterium chlorum, Mycoplasma capricolum , Bacteroides fragilis, Flavobacterium heparinum, Desulfovibrio desulfuricans, Myxococcus xan-VOL. 38,1988 PHYLOGENY OF CAMPYLOBACTER-LIKE ORGANISMS 59 thus, and Anacystis nidulans (11). Highly conserved regions were used for initial alignments.…”

Section: Methodsmentioning

confidence: 99%

“…Alignment of less conserved regions was aided by analysis of secondary structure. Helical and nonhelical regions were identified and aligned with corresponding regions of previously published sequences (11,46). Discrepancies in the expected secondary structure were verified or corrected by reexamining the sequencing autoradiographs.…”

Section: Methodsmentioning

confidence: 99%

“…rRNA sequencing appears to be the most powerful of these techniques and has proven to be highly effective in establishing both distant and close phylogenetic relationships among bacteria (23,45,47). Over 400 microorganisms have been analyzed by 16s rRNA oligonucleotide cataloging (45, 47), and 16s rRNAs from a few bacterial species have been completely sequenced (11). This technique has provided the basis for dividing eubacteria into 11 major phyla (45,47).…”

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confidence: 99%

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Phylogeny of Campylobacters, Wolinellas, Bacteroides gracilis, and Bacteroides ureolyticus by 16S Ribosomal Ribonucleic Acid Sequencing

Paster¹,

Dewhirst²

1988

International Journal of Systematic Bacteriology

229

198

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“…The following species were compared : Mycoplasma capricolum (Iwami et al, 1984), Mycoplasma strain PG 50 (Frydenberg & Christiansen, 1985), E. coli (Brosius et al, 1978), Proteus vulgaris (Carbon et al, 1981), Bacillus brevis, Bacillus stearothermophilus and Bacillus subtilis (Woese et al, 1983;Huysmans & De Wachter, 1986), and Xenopus laevis (Salim & Maden, 1981). The sequences correspond to the variable regions V3 (base 998-1043, Fig.…”

Section: U B Gobel a G E I S E R A N D E J S T A N B R I Dmentioning

confidence: 99%

Oligonucleotide Probes Complementary to Variable Regions of Ribosomal RNA Discriminate between Mycoplasma Species

Göbel

Geiser²,

Stanbridge³

1987

Microbiology

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On the basis of information from computer-assisted sequence comparison of the Mycoplasma pneumoniae 16s ribosomal RNA (rRNA) sequences with sequences from various other mycoplasmal and bacterial species, we constructed M. pneumoniae-specific oligonucleotide probes complementary to variable regions in the 16s rRNA molecule. Using a DNA/RNA dot blot hybridization procedure, it was possible to detect less than 1 x lo3 mycoplasmas. This test is a most sensitive assay for species-specific detection of bacteria. It can easily be adapted for detection and identification of other bacterial species and may have wide medical and industrial application.

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Compilation of small ribosomal sobunit RNA sequences

Cited by 76 publications

References 17 publications

In vivo translation of a region within the rrnB 16S rRNA gene of Escherichia coli

In vivo translation of a region within the rrnB 16S rRNA gene of Escherichia coli

Phylogeny of Campylobacters, Wolinellas, Bacteroides gracilis, and Bacteroides ureolyticus by 16S Ribosomal Ribonucleic Acid Sequencing

Oligonucleotide Probes Complementary to Variable Regions of Ribosomal RNA Discriminate between Mycoplasma Species

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