Although heat is known thermodynamically to unfold RNA in the test tube, the effect of heat stress on the global transcriptome within the complex environment of the living cell has not been investigated in any organism. We harnessed innovative methods for genome-wide probing of RNA structure in vivo to quantify the effect of heat shock on the RNA structurome in the eukaryote rice, a vitally important crop that is vulnerable to temperature stress. By coupling these assays with measurements of the temperature-regulated transcriptome and translatome, we reveal previously unknown relationships between temperature modulation of mRNA structure melting and mRNA abundance loss, with implications for crop improvement. RNA structure is known to influence numerous processes related to gene expression, but there have been few studies on the global RNA structurome as it prevails in vivo.
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Mazulkree Bacterial RNA thermometers: molecular zippers and switches — Semantic Scholar They encode the factor Zipper binding protein and Lst involved in lipopolysaccharide modification.
Probing RNA structure within living cells. The HrcA repressor is the thermosensor of the heat-shock regulatory circuit in the human pathogen Helicobacter pylori. Unwinding activity of cold shock proteins and RNA metabolism. The reversibility of the melting process permits simple bidirectional control of translation because the structure melts open and allows translation while the temperature increases, but refolds and blocks translation when the temperature drops again Chowdhury et al.
SHAPE could successfully probe the structure of the bqcterial HIV RNA genome leading to the identification of structural regions that interact with nucleocapsid proteins and elements important for nolecular regulation of viral gene expression Watts et al.
Regulation of heat-shock genes in bacteria: Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution. Translational control of small heat shock genes in mesophilic and thermophilic cyanobacteria by RNA thermometers. A In an in vitro approach, RNA is isolated from a cell culture and re-folded prior to treatment with single-stranded ss or double-stranded ds specific probes like nucleases P1 and S1 or RNase V1, respectively.
Liberation of the RBS permits formation of the translation initiation complex and translation occurs. The RNase V1 enzyme cleaves at double-stranded nucleotides. This approach unveiled the secondary structure profile of more than yeast transcripts and revealed interesting structural features, such as a higher average secondary structure occurrence in coding regions compared to untranslated regions, a three-nucleotide periodicity moldcular secondary structure across coding regions and correlation between translation efficiency and the structure around the translation start site Kertesz et al.
A novel DNA element that controls bacterial heat shock gene expression. Molecular basis for temperature sensing by an RNA thermometer. Secondary structure bactrial the ribosome binding site determines translational efficiency: You can login by using one of your existing accounts.
Translation on demand by a simple RNA-based thermosensor. Comparison between in vitro and in vivo data will ultimately provide a detailed picture of the RNA structurome in its physiological context.
RNA thermometer-mediated translational regulation. There was a problem providing the content you requested 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. RNA thermometers are common in alpha- and gamma-proteobacteria.
Another important aspect is that mmolecular folding process of a nascent bacterial Tgermometers is coupled to its transcription and translation. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome.
The sequencing reads are mapped to the reference genome or transcriptome and the position of each read along the transcript provides information on single- and double-stranded nucleotides. Transient RNA structure features are evolutionarily conserved and can be computationally predicted.
Thermomwters this case, a complex RNA population is cleaved or modified with structure-specific probes prior to cDNA synthesis and sequencing. A tricistronic heat shock operon is important for stress tolerance of Pseudomonas putida and conserved in many environmental bacteria. Topics Discussed in This Paper.
Upon treatment, modified or cut positions are mapped by polyacrylamide gel electrophoresis, if necessary after reverse transcription. Global analysis of RNA secondary structure in two metazoans. In vivo global structure probing strategies have been attempted only very recently and applied to A. First, only a single species of RNA can be tested per experiment, making this technique suitable for the validation of individual structures but not for global screening purposes. The use, distribution or reproduction in other forums is permitted, provided the original author s or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice.
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. Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers.
RNA secondary structure can also be sampled in vivo. A decade of riboswitches. TOP Related Posts.
Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance
Some RNATs act like zippers that open and close, in a reversible manner, according to the ambient temperature. These RNATs control heat shock and virulence genes. Escherichia coli uses a cascade of hierarchically organized RNATs to monitor any harmful temperature upshifts and to induce the production of protective heat shock proteins when required. Known heat shock RNATs have little if any sequence conservation. Recent biophysical approaches revealed details of RNAT zippers at base pair resolution. RNATs that permit translation of cold-shock and phage genes at low temperatures switch between two mutually exclusive structures.
How to find RNA thermometers
Transient RNA structure features are evolutionarily conserved and can be computationally predicted. The first reported RNAT are unique and rather complex. There was a problem providing the content you requested The reversibility of the melting process permits simple bidirectional control of translation because the structure melts open and allows translation while the temperature increases, but refolds and blocks translation when the temperature bacteriall again Chowdhury et al. You can login by using one of your existing accounts.