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.
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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. The conformation at low temperature favours translation. Synthetic thermosensors inspired by natural RNATs can induce gene expression in response to a temperature upshift and bear potential as tools for large-scale industrial applications without the need for chemical inducers.
Abstract Bacteria use complex strategies to coordinate temperature-dependent gene expression. Increasing the temperature gradually shifts the equilibrium between the closed and open conformations towards the open structure in a zipper-like manner, thereby increasing the efficiency of translation initiation.
We also discuss RNA-based thermosensors located upstream of cold shock and other genes, translation of which preferentially occurs at low temperatures and which thus operate through a different, more switch-like mechanism. Finally, we consider the potential biotechnological applications of natural and synthetic RNATs.
Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance
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. Moreover, how heat shock rapidly affects RNA structure genome-wide in living systems remains unknown. We report here in vivo heat-regulated RNA structuromes. We show that RNA secondary structure broadly regulates gene expression in response to heat shock in this essential crop species.
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. A single short stem-loop structure can be sufficient to confer thermoregulation, as shown for the nt long hsp17 RNAT from Synechocystis sp. Skip to search form Skip to main content. A tricistronic heat shock operon is important for stress tolerance of Pseudomonas putida and conserved in many environmental bacteria.
Bacterial RNA thermometers: molecular zippers and switches
Among the many ways to register temperature changes, bacteria often use temperature-modulated structures in the untranslated region of mRNAs. 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. Base pairing of proximal nucleotides generates secondary structures, like stem-loops. Long distance interactions allow formation of tertiary structures, like pseudoknots or kissing loops.
How to find RNA thermometers
Shaktidal The genome-wide assessment of RNA structures relies on structure-probing techniques able to distinguish single- and double-stranded regions. B The in vivo approach allows to probe native RNA structures directly inside the cell using chemical probes that penetrate the membranes and modify nucleotides in a ss conformation. Virulence Thermommeters Device Component Ribosomes. However, while computational methods are advanced enough to accurately predict short and stable secondary structures, their reliability decreases substantially with increasing length of the RNA molecule or when complex structures, such as pseudoknots and other tertiary interactions, come into play. RNA thermometer-mediated translational regulation. Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence.