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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Two identical RNATs were found upstream of the Leptospira interrogans virulence genes ligA and ligB coding for putative lipoproteins important for adhesion and complement resistance Matsunaga et al. This structure is much weaker in the mutated RNA. Since then numerous RNAT-controlled heat shock and virulence genes have been discovered. Advances in RNA structure analysis by chemical probing.
From This Paper Figures, tables, and topics from this paper. Swjtches and automation of sequencing-based characterization of RNA structure. In vivo genome-wide profiling of RNA molecuular structure reveals novel regulatory features.
Mo,ecular that the principle has been established in yeast Wan et al. The HrcA repressor is the thermosensor of the heat-shock regulatory circuit in the human pathogen Helicobacter pylori. Structured RNA elements are known to respond to different stimuli, for example metabolite-sensing riboswitches Serganov and Nudler, A switcges thermosensor controls expression of rhizobial heat shock genes. Upon treatment, modified or cut positions are mapped by polyacrylamide gel electrophoresis, if necessary after reverse transcription.
Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans.
Structural data can be used to constrain RNA structure prediction algorithms in order to obtain more accurate mloecular secondary structure models of all the sequenced transcripts. You can login by using one of your existing accounts. These regions might have a role in temperature-mediated post-transcriptional gene regulation. Therefore, unbiased experimental high-throughput approaches are desirable for the identification of regulatory RNA structures on a global scale.
After library preparation and deep sequencing, the resulting reads are mapped to the reference genome or transcriptome. Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence.
Bacterial RNA thermometers: molecular zippers and switches – Wikidata
We will be provided with an authorization token please note: Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-blooded host. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential zippwrs of interest. Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers. A widely used probe is DMS, which methylates unpaired adenine and cytosine bases.
Quite surprisingly, no prokaryotic RNA structurome has been reported so far. Genome-wide measurement of RNA folding energies. Together, in vivo and in vitro data provide valuable complementary information to unveil biologically relevant structures and their dynamics.
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 molefular compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions and correlation between translation efficiency and switcues structure around the translation start site Kertesz et al. Bacterial riboswitches and RNA thermometers: Temperature-driven differential gene expression by RNA thermosensors.
It is easily conceivable that temperature-responsive 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. 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.
In vivo structure probing averages the structural state of each nucleotide from all conformations the RNA molecule adopts during its life cycle.
Temperature-controlled structural alterations of an RNA thermometer. Temperature sensing in Yersinia pestis: Translation on demand by a simple RNA-based thermosensor.
These approaches are well established and were successfully applied in the theermometers analysis of a wide range of RNA molecules. Not only the sequence but also the overall architecture differs substantially among presently known RNAT. High-throughput genome-wide RNA structure probing.
Use of dimethyl sulfate to probe RNA structure in vivo. Long and complex structures involving regions in both the untranslated and coding regions are used to permit translation at low temperature.
Although often successful, this approach is laborious because every RNAT candidate must be experimentally validated, for example by reporter gene fusions, typically in E. Pubmed Abstract Pubmed Full Text. Understanding the transcriptome through RNA structure. In vivo global structure probing strategies have been attempted only very recently and applied to A.
Bacterial RNA thermometers: molecular zippers and switches – Semantic Scholar
The first reported RNAT are unique and rather complex. Base pairing of proximal nucleotides generates secondary structures, like stem-loops. Topics Discussed in This Paper. A decade of riboswitches. A novel DNA element that controls bacterial heat shock gene expression. Katherine E DeiganAdrian R. ROSE elements occur in disparate rhizobia and are functionally interchangeable between species.
In this case, a complex RNA population is cleaved or modified with structure-specific probes prior to cDNA synthesis and sequencing.