The sequence of the 6S RNA gene of<i>Pseudomonas aeruginosa</i>

Vogel, Detlef W.; Hartmann, Roland K.; Struck, Joachim; Ulbrich, Norbert; Erdmann, Volker A.

doi:10.1093/nar/15.11.4583

Cited by 28 publications

(13 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…On the 5′-side, several clones had their 5′ end 5–6 nt downstream of the pheT stop codon (Figure 3). Assuming that the mature 5′ end of 6S RNA roughly coincides with the pheT stop codon, we considered the mature 6S RNA homolog to have a length of ∼150 nt, thus somewhat shorter than the size of 6S RNAs from E.coli and Pseudomonas aeruginosa [∼185 nt (22–24)]. Despite this length difference, mfold analysis predicted a rod-shaped secondary structure for the A.aeolicus RNA, with astounding similarity to the proposed structure of E.coli 6S RNA (Figure 4A; for details see Discussion).…”

Section: Resultsmentioning

confidence: 99%

Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog

Willkomm

Minnerup²,

Hüttenhofer³

et al. 2005

Nucleic Acids Research

View full text Add to dashboard Cite

By an experimental RNomics approach, we have generated a cDNA library from small RNAs expressed from the genome of the hyperthermophilic bacterium Aquifex aeolicus. The library included RNAs that were antisense to mRNAs and tRNAs as well as RNAs encoded in intergenic regions. Substantial steady-state levels in A.aeolicus cells were confirmed for several of the cloned RNAs by northern blot analysis. The most abundant intergenic RNA of the library was identified as the 6S RNA homolog of A.aeolicus. Although shorter in size (150 nt) than its γ-proteobacterial homologs (∼185 nt), it is predicted to have the most stable structure among known 6S RNAs. As in the γ-proteobacteria, the A.aeolicus 6S RNA gene (ssrS) is located immediately upstream of the ygfA gene encoding a widely conserved 5-formyltetrahydrofolate cyclo-ligase. We identifed novel 6S RNA candidates within the γ-proteobacteria but were unable to identify reasonable 6S RNA candidates in other bacterial branches, utilizing mfold analyses of the region immediately upstream of ygfA combined with 6S RNA blastn searches. By RACE experiments, we mapped the major transcription initiation site of A.aeolicus 6S RNA primary transcripts, located within the pheT gene preceding ygfA, as well as three processing sites.

show abstract

Section: Resultsmentioning

confidence: 99%

Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog

Willkomm

Minnerup²,

Hüttenhofer³

et al. 2005

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Bacteria contain numerous small regulatory RNAs (sRNAs) ranging in size from 70 to 500 nucleotides (nt) that modulate gene expression (Vogel et al, 1987), similarity with a known sRNA of E. coli (Toschka et al, 1989), computational predictions ) and copurification with a protein . Three systematic searches for sRNAs have been undertaken in P. aeruginosa, where all have focused on intergenic regions.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide identification of novel small RNAs in Pseudomonas aeruginosa

Gómez-Lozano

Marvig

Molin

et al. 2012

Environmental Microbiology

101

109

View full text Add to dashboard Cite

Summary Bacterial small regulatory RNAs (sRNAs) function in post‐transcriptional control of gene expression and control a variety of processes including metabolic reactions, stress responses and pathogenesis in response to environmental signals. A variety of approaches have been used previously to identify 44 sRNAs in the opportunistic human pathogen Pseudomonas aeruginosa. In this work, RNA sequencing (RNA‐seq) is used to identify novel transcripts in P. aeruginosa involving a combination of three different sequencing libraries. Almost all known sRNAs and over 500 novel intergenic sRNAs are identified with this approach. Although the use of three libraries increased the number of novel transcripts identified, there were significant differences in the subset of transcripts detected in each library, underscoring the importance of library preparation strategy and relative sRNA abundance for successful sRNA detection. Nearly 90% of the novel sRNAs have no orthologous bacterial sequences outside of P. aeruginosa, supporting a limited degree of sequence conservation and rapid evolution of sRNAs at the species level. We anticipate that the data will be useful for the study of regulatory sRNAs in bacteria and that the approach described here may be applied to identify sRNAs in any bacterium under different growth and stress conditions.

show abstract

“…Although E. coli 6S RNA was the first noncoding RNA to be sequenced >30 yr ago (Brownlee 1971), additional 6S RNA homologs have only been reported in Pseudomonas aeruginosa (Vogel et al 1987) and Haemophilus influenzae (Brosius 1996). All currently known 6S RNA sequences identified by bioinformatics in the Rfam database are likewise restricted to species of ␥-proteobacteria (GriffithsJones et al 2003).…”

Section: Introductionmentioning

confidence: 99%