Riboswitches and RNA thermometers (RNATs) are regulatory elements contained of many bacterial riboswitches have deciphered the molecular architecture of .. to complete translation of downstream gene in a zipper like fashion . Fig. Bacterial RNA thermometers: molecular zippers and switches (English). 0 references. author name string. Jens Kortmann. series ordinal. 1. 3 Catalytic RNAs RNA binds metal ions that function Kortmann J, Narberhaus F. Bacterial RNA thermometers: molecular zippers and switches.
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RNA secondary structure can also be sampled in vivo.
Virulence Cascade Device Component Ribosomes. Secondary structure of the ribosome bacteral site determines translational efficiency: The melting temperature of each sequenced transcript was measured at a single nucleotide resolution, which led to the identification of RNA regions that undergo conformational changes in a physiological range of temperature. Cotranscriptional folding and the progressive binding of proteins and ribosomes guide the folding into secondary structures that can differ from the structure of an RNA molecule folded and probed in vitro.
Bacterial RNA thermometers: molecular zippers and switches – Wikidata
The prfA gene encodes a transcription factor that controls the synthesis of a number of important virulence factors. All these approaches were based on the treatment of living cells with DMS, a chemical probe that can quickly cross the membranes and modify preferentially unpaired adenine and cytosine residues. The prfA thermosensor is peculiar as it integrates not only the temperature signal by structural changes but also metabolic information via a riboswitch-derived small regulatory RNA Loh et al.
Genome-wide measurement of RNA secondary switchfs in yeast. You can login by using one of your existing accounts. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome.
Regulation of heat-shock genes in bacteria: Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-blooded host. The bioinformatic analysis of the raw data is a challenge and considerable effort has been put on switchex development in order to facilitate data interpretation Aviran et al. From This Paper Figures, tables, and topics from this paper.
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Topics Discussed in This Paper. Bacterial riboswitches and RNA thermometers: Increasing or decreasing temperatures sqitches the conformation of that structure, allowing or preventing ribosome access and thus translation. Almost simultaneously, the first RNAT-regulated virulence gene was described in Listeria monocytogenes Johansson et al. Conserved nucleotides upstream of the open reading frame were first believed to serve as binding site for a temperature-responsive transcription factor Narberhaus et al.
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. SHAPE could successfully probe the structure of the 9-kb HIV RNA genome leading to the identification of structural regions that interact with nucleocapsid proteins and elements important for the regulation of viral gene expression Watts et al.
Frontiers | How to find RNA thermometers | Cellular and Infection Microbiology
Base pairing of proximal nucleotides generates secondary structures, like stem-loops. These regions might have a role in temperature-mediated post-transcriptional gene regulation. Given that the principle has been established in yeast Wan et al. Modified bases block reverse transcription and sequencing of the resulting fragments permits the identification of the reactive sites and the mapping of single-stranded nucleotides.
The first pioneering studies took advantage of structure-specific enzymatic probes. Direct observation of the temperature-induced melting process thermometefs the Salmonella fourU RNA thermometer at base-pair resolution. Suggest a Research Topic. Structural data anv be used to constrain RNA zoppers prediction algorithms in order to obtain more accurate experimentally-derived secondary structure models of all the sequenced transcripts. B The in vivo approach allows to probe native RNA structures directly inside the cell using chemical probes that penetrate the bactetial and modify nucleotides in a ss conformation.
Temperature sensing is based on several non-canonical, heat-labile base pairs Chowdhury et al. Only recently high-throughput sequencing technologies have been successfully applied to RNA structure probing in order to obtain experimentally-derived genome-wide insights into RNA folding.
Advances in RNA structure analysis by chemical probing. Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans. Together, in vivo and in vitro data provide valuable complementary information to unveil biologically relevant structures and their dynamics.
Sangita Phadtare RNA biology Molecular basis for temperature sensing by an RNA thermometer. After DMS treatment, the RNA is isolated and the modification position is detected by reverse transcription and deep sequencing.
This approach unveiled the bactetial structure profile of more than yeast transcripts and revealed interesting structural gna, such as a higher average secondary structure occurrence in coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions and correlation between translation efficiency and the structure around the translation start site Kertesz et al.
It is easily conceivable that aippers structures such as RNATs can be discovered by this technology and a first step in this direction has been undertaken by probing the whole yeast transcriptome at different temperatures Wan et al.
Bacterial RNA thermometers: molecular zippers and switches
Landscape and variation swtches RNA secondary structure across the human transcriptome. After establishing that 38 transcription factors did not control cssA expression, it emerged that an RNA structure is responsible for this effect.
In this article, we describe how such RNA thermometers RNATs have been discovered one by one upstream of heat shock and virulence genes in the past, and how next-generation sequencing approaches are able to reveal novel temperature-responsive RNA structures on a global scale.
This approach permits the identification of ss regions only. Mfold web server for nucleic acid folding and hybridization prediction. It will be particularly interesting to learn whether RNATs exist in other places than heat shock and virulence gene transcripts.