Primary sequence of the 16S ribosomal RNA of Escherichia coli

Ehresmann, Chantal; Stiegler, Patrick; Mackie, George A.; Zimmermann, Robert A.; Ebel, Jean Pierre; Fellner, Peter

doi:10.1093/nar/2.2.265

Cited by 107 publications

(83 citation statements)

References 42 publications

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“…To identify optimal SD sequences for our expression vectors, we used the Bacteroidales genome sequences available in public databases. Figure 1A shows alignment of the 3= ends of the 16S rRNA gene sequences extracted from the genome sequences of Bacteroides thetaiotaomicron VPI 5482 (29), Bacteroides vulgatus ATCC 8482 (30), Bacteroides ovatus V975 (U. Wegmann, unpublished data), Bacteroides fragilis NCTC 9343 (30), Prevotella denticola F0289 (CP002589), and Prevotella bryantii B14 (31) with the sequenced 3= ends of 16S rRNA sequences from Escherichia coli (32,33), Bacillus subtilis (34), Bacillus stearothermophilus (35) (now Geobacillus stearothermophilus), and Lactococcus lactis (36), which demonstrates the perfect sequence conservation with regard to the 3= ends of the 16S rRNAs. In the cases of B. thetaiotaomicron, B. vulgatus, P. denticola, and P. bryantii, the 16S rRNA genes annotated in the respective genomes were extended with additional downstream sequence data on the basis that all rRNA gene operons present in the genome were followed by the same stretch of sequence that would be transcribed into the same 3= ends as those reported for Gram-positive 16S rRNA sequences.…”

Section: Resultsmentioning

confidence: 99%

Defining the Bacteroides Ribosomal Binding Site

Wegmann¹,

Horn²,

Carding

2013

Appl Environ Microbiol

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The human gastrointestinal tract, in particular the colon, hosts a vast number of commensal microorganisms. Representatives of the genus Bacteroides are among the most abundant bacterial species in the human colon. Bacteroidetes diverged from the common line of eubacterial descent before other eubacterial groups. As a result, they employ unique transcription initiation signals and, because of this uniqueness, they require specific genetic tools. Although some tools exist, they are not optimal for studying the roles and functions of these bacteria in the human gastrointestinal tract. Focusing on translation initiation signals in Bacteroides, we created a series of expression vectors allowing for different levels of protein expression in this genus, and we describe the use of pepI from Lactobacillus delbrueckii subsp. lactis as a novel reporter gene for Bacteroides. Furthermore, we report the identification of the 3= end of the 16S rRNA of Bacteroides ovatus and analyze in detail its ribosomal binding site, thus defining a core region necessary for efficient translation, which we have incorporated into the design of our expression vectors. Based on the sequence logo information from the 5= untranslated region of other Bacteroidales ribosomal protein genes, we conclude that our findings are relevant to all members of this order.

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Section: Resultsmentioning

confidence: 99%

Defining the Bacteroides Ribosomal Binding Site

Wegmann¹,

Horn²,

Carding

2013

Appl Environ Microbiol

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“…Part of the PCR results are shown in Figs 1 and 2. Kiss et al (1977) reported that there are several rRNA operons (rRNA A : G) for E. coli cells while Ehresmann et al (1975) reported the heterogeneity in 16S rRNA sequences for E. coli. Thus, data in Table 3 may imply that for all E. coli strains, the 16E1 target sequence is present in the V 3 region.…”

Section: Detection Specificity For Primer Sets Of 16e1/16e2 16e1/16ementioning

confidence: 99%

Development and use of 16S rRNA gene targeted PCR primers for the identification of Escherichia coli cells in water

Tsen

Lin

Chi

1998

Journal of Applied Microbiology

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I . 1998. The primary sequences of the V 3 and V 6 regions of the 16S rRNA gene of pathogenic and non-pathogenic strains of Escherichia coli were determined and compared with those obtained for a number of reference strains which belong to the family Enterobacteriaceae. Three oligonucleotide primers 16E1, 16E2 and 16E3 were designed and used in the polymerase chain reaction to identify specifically all E. coli isolates. When 16E1, 16E2 and 16E3 were used as primers for the identification of E. coli cells present in tap, underground and pond waters, as low as 1 cfu 100 ml −1 of water could be detected if an 8 h pre-culture step was performed prior to the PCR reaction.

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“…The generally rather weak cross-linking by formaldehyde of the RNA binding proteins in the 30-S subunit has already been commented upon in the previous section, and several other proteins are either very weakly linked or not observable (see Table 16 16-S R N A . The 16-S RNA is divided into sections as in [36]. Nucleotide sequences contained in ribonucleoprotein fragment 11 are described in the following paper [21] and those from fragment 111 in [5] 2).…”

Section: Analysis Of 30-s Subunit Rna Regionsmentioning

confidence: 99%

The Use of Formaldehyde in RNA‐Protein Cross‐linking Studies with Ribosomal Subunits from Escherichia coli

Möller

Rinke

Ross

et al. 1977

European Journal of Biochemistry

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Radioactive subunits from Escherichia coli ribosomes were treated with formaldehyde, with a view to inducing a controlled cross-linking reaction between protein and ribosomal RNA. Under the conditions described, about 10-15 of the total protein remained bound to the RNA in the presence of dodecyl sulphate, and little or no irreversible protein-protein cross-linking was observed. The RNA-protein complexes are of a rather unstable nature, and the reaction is spontaneously reversible.The proteins involved in the cross-linked complexes were examined by polyacrylamide gel electrophoresis, after removal of unbound protein and nuclease treatment to digest the RNA-protein complex. This showed that the individual ribosomal proteins were cross-linked to varying degrees, and most of the proteins were involved in the reaction at least to some extent. A distinct group of proteins from each subunit were, however, reproducibly cross-linked in high yield.The formaldehyde-treated subunits were subjected to a controlled hydrolysis with ribonuclease TI, and RNA fragments of known nucleotide sequence containing the cross-linked proteins were isolated. Despite the reversibility of the cross-linking reaction, sufficient cross-linked protein survived the experiment to enable an analysis to be made of proteins associated with the various RNA fragments.In the 50-S subunit, proteins L27 and L32 were found to be cross-linked to the 18-S RNA fragment which arises from the 3' end of 23-S RNA. L2, L6 and L16 were also found in this fragment in small amounts. In contrast, L13 appeared to be linked to both the 18-S RNA and the 13-S RNA fragment from the 5' end of 23-S RNA. In the 30-S subunit, proteins S3, S5, S9 (ll), S 13, and to some extent S4, S7, S 12 and S 18, were found associated with an RNA region comprising approximately 900 nucleotides at the 5' end of 16-S RNA. S4, S9 (ll), S13, and to a lesser extent S 7 and S14, were found in an RNA region comprising about 450 nucleotides near the 3' end of 16-S RNA, but lacking the 3'-terminal 150 nucleotides. Protein S21 was cross-linked to 16-S RNA, but was not found in either of the two RNA regions above.Two different biochemical approaches are currently being used to investigate RNA-protein interactions in the Escherichia coli ribosome. The first of these involves the study of complexes between isolated proteins and ribosomal RNA or fragments of ribosomal , and this method is basically intended to discover those regions of the RNA which contain stable 'binding sites' for individual proteins. The second approach involves the isolation of ribonucleoprotein fragments from ribosomal subunits, the purpose here being to investigate topographical relationships 'between proteins or groups

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Primary sequence of the 16S ribosomal RNA of Escherichia coli

Cited by 107 publications

References 42 publications

Defining the Bacteroides Ribosomal Binding Site

Defining the Bacteroides Ribosomal Binding Site

Development and use of 16S rRNA gene targeted PCR primers for the identification of Escherichia coli cells in water

The Use of Formaldehyde in RNA‐Protein Cross‐linking Studies with Ribosomal Subunits from Escherichia coli

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