ArticleNucleic acids research2005
Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 57 citations in OpenAlex.
- Characterization of RNA-based and protein-only RNases P from bacteria encoding both enzyme types.RNA (New York, N.Y.) · 2023Article
- Structural and Functional Insight into the Mechanism ofNon-coding RNA · 2022Article
- 6S-Like scr3559 RNA Affects Development and Antibiotic Production inMicroorganisms · 2021Article
- 6S-2 RNA deletion in the undomesticatedRNA biology · 2021Article
- The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic EngineerJournal of bacteriology · 2019Article
- 6S RNA, a Global Regulator of Transcription.Microbiology spectrum · 2018Review
- Thermodynamic matchers for the construction of the cuckoo RNA family.RNA biology · 2015Article
- NifA- and CooA-coordinated cowN expression sustains nitrogen fixation by Rhodobacter capsulatus in the presence of carbon monoxide.Journal of bacteriology · 2014Article
- Genomewide comparison and novel ncRNAs of Aquificales.BMC genomics · 2014Article
- Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems.RNA biology · 2014Review
- Dissemination of 6S RNA among bacteria.RNA biology · 2014Article
- Translational control of small heat shock genes in mesophilic and thermophilic cyanobacteria by RNA thermometers.RNA biology · 2014Article
- Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet.Acta crystallographica. Section F, Structural biology and crystallization communications · 2013Article
- Article
- Bacterial small RNA regulators: versatile roles and rapidly evolving variations.Cold Spring Harbor perspectives in biology · 2011Review
- Rho-dependent termination of ssrS (6S RNA) transcription in Escherichia coli: implication for 3' processing of 6S RNA and expression of downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase).The Journal of biological chemistry · 2011Article
- Discovery of a minimal form of RNase P in Pyrobaculum.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.PLoS genetics · 2008Article
- Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021.BMC genomics · 2007Article
- A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.PLoS computational biology · 2007Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 gamma-proteobacterial homologs (approximately 185 nt), it is predicted to have the most stable structure among known 6S RNAs. As in the gamma-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 gamma-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.
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