ArticleMolecular genetics and genomics : MGG2007
Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers.
Article in Molecular genetics and genomics : MGG, 2007. 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, 54 citations in OpenAlex.
- Mechanisms of thermoregulation inJournal of bacteriology · 2026Review
- Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX.Nucleic acids research · 2025Article
- Robo-Therm, a pipeline to RNA thermometer discovery and validation.RNA (New York, N.Y.) · 2024Article
- Temperature-sensing riboceptors.RNA biology · 2024Article
- An RNA thermometer in the chloroplast genome of Chlamydomonas facilitates temperature-controlled gene expression.Nucleic acids research · 2023Article
- Developing New Tools to Fight Human Pathogens: A Journey through the Advances in RNA Technologies.Microorganisms · 2022Review
- Exploiting RNA thermometer-driven molecular bioprocess control as a concept for heterologous rhamnolipid production.Scientific reports · 2021Article
- Evaluating temperature-induced regulation of a ROSE-like RNA-thermometer for heterologous rhamnolipid production in Pseudomonas putida KT2440.AMB Express · 2019Article
- RNA Thermometers in Bacterial Pathogens.Microbiology spectrum · 2018Review
- Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions.Nucleic acids research · 2017Article
- RNAiFold2T: Constraint Programming design of thermo-IRES switches.Bioinformatics (Oxford, England) · 2016Article
- Tet-Trap, a genetic approach to the identification of bacterial RNA thermometers: application to Pseudomonas aeruginosa.RNA (New York, N.Y.) · 2014Article
- Regulation of Pseudomonas aeruginosa virulence factors by two novel RNA thermometers.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- How to find RNA thermometers.Frontiers in cellular and infection microbiology · 2014Review
- RNAthermsw: direct temperature simulations for predicting the location of RNA thermometers.PloS one · 2014Article
- Potential thermosensitive riboswitches in the genome of Salmonella.Cytology and genetics · 2013Article
- Search for the new potential RNA thermometers in the genome ofMicrobiology · 2013Article
- Bacterial RNA thermometers: molecular zippers and switches.Nature reviews. Microbiology · 2012Review
- Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence.PLoS pathogens · 2012Article
- LacI(Ts)-regulated expression as an in situ intracellular biomolecular thermometer.Applied and environmental microbiology · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Only recently, the fundamental role of regulatory RNAs in prokaryotes and eukaryotes has been appreciated. We developed a pipeline from bioinformatic prediction to experimental validation of new RNA thermometers. Known RNA thermometers are located in the 5'-untranslated region of certain heat shock or virulence genes and control translation by temperature-dependent base pairing of the ribosome binding site. We established the searchable database RNA-SURIBA (Structures of Untranslated Regions In BActeria). A structure-based search pattern reliably recognizes known RNA thermometers and predicts related structures upstream of annotated genes in complete genome sequences. The known ROSE(1) (Repression Of heat Shock gene Expression) thermometer and several other functional ROSE-like elements were correctly predicted. For further investigation, we chose a new candidate upstream of the phage shock gene D (pspD) in the pspABCDE operon of E. coli. We established a new reporter gene system that measures translational control at heat shock temperatures and we demonstrated that the upstream region of pspD does not confer temperature control to the phage shock gene. However, translational efficiency was modulated by a point mutation stabilizing the predicted hairpin. Testing other candidates by this structure prediction and validation process will lead to new insights into the requirements for biologically active RNA thermometers. The database is available on http://www.ruhr-uni-bochum.de/mikrobiologie/ .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.