RNA thermometers (RNATs) modulate translation efficiency of an mRNA according to the .. Bacterial RNA thermometers: molecular zippers and switches . Nat. RNA thermometers mediate responses to temperature changes in various .. Bacterial RNA thermometers: molecular zippers and switches. Bacterial 'RNA thermometers' – basic roles and mechanisms. The importance of RNA of bacteria. RNATs, whether they involve zipper or switch mechanisms.
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Bacterial RNA thermometers: Molecular zippers and switches. Article· Literature Review (PDF Available) in Nature Reviews Microbiology 10(4) · March. Changes in the structure and dynamics of MiniROSE RNA, which regulates translation in the Bacterial RNA thermometers: molecular zippers and switches. Download PDFDownload. Share Riboswitches and RNA thermometers ( RNATs) are regulatory elements Sequences and structural studies of many bacterial riboswitches have deciphered the molecular architecture of aptamers at atomic levels. .. to complete translation of downstream gene in a zipper like fashion .
The commonly accepted molecular mechanism for riboswitch function proposes a ligand-dependent conformational switch between two mutually exclusive states 4. According to this mechanism, ligand binding to an aptamer domain induces an allosteric conformational switch of an expression platform, leading to activation or repression of ligand-related gene expression 5. However, many riboswitch properties cannot be explained by a pure two-state mechanism. Here we show that the regulation mechanism of the adenine-sensing riboswitch, encoded by the add gene on chromosome II of the human Gram-negative pathogenic bacterium Vibrio vulnificus 6 , is notably different from a two-state switch mechanism in that it involves three distinct stable conformations. The observed temperature dependence of a pre-equilibrium involving two structurally distinct ligand-free conformations of the add riboswitch conferred efficient regulation over a physiologically relevant temperature range.
Also known as RNA thermosensors, these temperature-sensitive segments of the mRNA regulate gene expression by changing their secondary structure in response to temperature fluctuations.
The detection of RNA thermometers in various genes of interest is valuable as it could lead to the discovery of new thermometers participating in fundamental processes such as preferential translation during heat-shock. RNAthermsw is a user-friendly webserver for predicting the location of RNA thermometers using direct temperature simulations. It operates by analyzing dotted figures generated as a result of a moving window that performs successive energy minimization folding predictions.
Inputs include the RNA sequence, window size, and desired temperature change. The website contains a help page with explanations regarding the exact usage. This is an open-access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Introduction RNA thermometers are temperature-sensitive RNAs that regulate gene expression and have recently attracted growing attention .
They are also known as RNA thermosensors and in general, they alter their secondary structure in response to temperature fluctuations. Together with riboswitches  ,  , these peculiar RNA switches are used as examples in support of the RNA world hypothesis.
RNA thermometers typically regulate genes required during either a heat shock or a cold shock response, but have implicated in other regulatory roles such as in pathogenicity and starvation .
Their conformational change and 3D structure have also been investigated  , . Bioinformatics search methods have been used to identify novel candidate RNA thermometers . Structure-based methods are needed for RNA thermometers because phylogenetic comparisons showed that the secondary structure of the temperature-sensitive RNA element is much more conserved than the nucleic acid sequence .
Thus, bioinformatic search methods for RNA thermometers should be focused on structural properties rather than on the sequence. The search in this database was completely independent of the primary sequence.
Storage of structures in RNA-SURIBA involved RNA secondary structure prediction by energy minimization using mfold  and dot bracket annotation together with relevant characteristics such as number of hairpins and bulges. Database search was performed with regular expression for the dot bracket annotation combined with structural features.
However, the approach is limited to searching a database composed of known RNA thermometers with their corresponding structures. Here, relying on energy minimization as in  but also including prediction of temperature changes, a simulation of heat-shock and cold-shock is performed. Energy minimization studies with temperature changes using the Vienna RNA package  for exploring synthetic and natural RNA thermometers have been performed before  ,  , but not for attempting to identify locations of RNA thermometers.
The initial program was reported in  and is conceptually based on a sliding window with local folding predictions performed inside the moving window, as in . These mutations are predicted to stabilize the RNA thermometer.
The reduction in reactivity was observed not only for nucleotides in the lower stem, but also for nucleotides in the upper stem, supporting a cooperative melting transition for the entire hairpin. However, introduction of neither C—G base pair had as profound an effect as the outright removal of the C bulge Fig. We then performed reporter assays in order to correlate changes in thermometer structure and stability with effects on thermometer function in bacterial cells.
This reporter system has been validated for study of RNA thermometers, including htrA Klinkert et al. These results were consistent with previous observations Klinkert et al. The mutant U25C element led to reduced expression at both temperatures compared to the wild-type thermometer, suggesting that it more effectively sequestered the SD sequence from interactions with ribosomal rRNA. These results suggest that the upper and lower stems share a common melting transition, again supporting cooperative melting behavior of the entire thermometer hairpin.
Many questions remain regarding the range of structural features that will lead to thermometer behavior Kortmann and Narberhaus Here, we performed an in-depth study of the S. Although HtrA is essential for response to heat shock in E. Here, we used SHAPE analysis and mutagenesis to investigate the structure, dynamics, and temperature response of the htrA thermometer.
We then went on to investigate the mechanism of thermometer melting.
We initially hypothesized that the bulged C might provide the nucleation point for a gradual melting of the entire stem with increasing temperature. This would parallel what has been observed with RNA thermometers such as the ROSE1 element from Bradyrhizobium japonicum, the cyanobacterial hsp17 thermometer, and the CssA thermometer from Neisseria meningitidis, for which thermometer melting occurs progressively from a destabilizing element upon temperature increase Chowdhury et al.
An alternative hypothesis was that the bulge would decouple the upper and lower stem into two independently folding units, with distinct melting transitions based on their individual stability. SHAPE assays performed on stem mutants of the htrA thermometer further support communication between the upper and lower stems, despite the intervening bulge. Mutations which strengthened base-pairing in the upper stem also increased the melting temperature of the lower stem, and vice versa Fig.
A cooperative melting transition is also observed in the agsA fourU thermometer from S. It is tempting to speculate that the combination of the single-nucleotide bulge and the cooperativity displayed between the stems of the htrA thermometer allows for tuning of the temperature response of the thermometer in response to the body temperature of the host.
Increased stability is experimentally evident through a shift in the melting temperature for nucleotides throughout the hairpin stem. Intermediate reactivities are observed when stabilizing mutations are introduced to the stem itself, even in the presence of the single-nucleotide bulge Fig.
Intriguingly, several nucleotides from the wild-type thermometer showed decreased reactivity upon temperature increase. If this is the situation for the final loop nucleotide, the decrease in reactivity at higher temperatures could be explained by thermometer melting, which would release it from the reactive conformation.
A similar effect might be responsible for the behavior of the bulged C nucleotide, which also displays decreased reactivity at increased temperatures. Reactivity levels again increase under the highest temperatures studied data not shown. However, higher reactivity levels at low temperatures might simply be a result of greater flexibility of this nucleotide in the single-nucleotide bulge than in the alternate hairpin.
Formation of the alternate hairpin also explains the decrease in reactivity observed for the G that precedes the standard thermometer stem Figs.
Further work will address the importance of this alternate hairpin, as well as the identity of the bulged nucleotide and its flanking base pairs, on thermometer behavior and function.
The presence of structured elements upstream of the thermometer at both temperatures is suggestive of additional function for this region, potentially allowing for combinatorial regulation of HtrA expression by both temperature and a yet-unknown signal.
The additional upstream sequence is highly conserved among Salmonella strains Supplemental Fig.