BACTERIAL RNA THERMOMETERS MOLECULAR ZIPPERS AND SWITCHES PDF

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 [70]. 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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Temperature triggers immune evasion by Neisseria meningitidis. In vivo structure probing averages the structural state of each nucleotide from all conformations the RNA molecule adopts during its life cycle. Liberation of the RBS permits formation of the translation initiation complex and translation occurs. High-throughput genome-wide RNA structure probing.

Regulation of heat-shock genes in bacteria: 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. Second, only a relatively short region of several nucleotides of an in vitro synthesized saitches labeled RNA can be investigated. RNA thermometer-mediated translational regulation.

Switcues Publications citing this paper. Hydroxyl radicals thermmometers at RNA bases that are solvent-exposed. RNA secondary structure can also be switcehs in vivo. When it comes to the identification of new regulatory RNA structures, classic structure probing techniques suffer from a couple of limitations.

Long distance interactions allow formation of tertiary structures, like pseudoknots or kissing loops. 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.

Temperature-driven differential gene expression by RNA thermosensors. Topics Discussed in This Paper. 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. RNA thermometers are common in alpha- and gamma-proteobacteria.

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PCC Kortmann et al. Pubmed Abstract Pubmed Full Text. The first pioneering studies took advantage of structure-specific anx probes. Long and complex structures involving regions in both the untranslated and coding regions are used to permit translation at low temperature.

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After library preparation and deep sequencing, the resulting reads are mapped to the reference genome or transcriptome. LacI Ts -regulated expression as an in situ intracellular biomolecular thermometer. 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.

Base pairing of proximal nucleotides generates secondary structures, like stem-loops.

Bacterial RNA thermometers: molecular zippers and switches – Semantic Scholar

The conformational switch affects the translatability and stability of the mRNA resulting in massive induction of the cold shock protein CspA at low temperatures Yamanaka et al. This approach could successfully confirm single-strand regions of non-coding RNA with known structure and unveiled the secondary structure of non-coding RNA with previously unknown structure Underwood et al. B The in vivo approach allows to thermometeers native RNA structures directly inside the cell using chemical probes that penetrate the membranes and modify nucleotides in a ss conformation.

Translation on demand by a switchs RNA-based thermosensor. Thermogenetic tools to monitor temperature-dependent gene expression in bacteria. 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.

We will be provided with an authorization token please note: Transient RNA structure features are evolutionarily conserved and can be computationally predicted. In this article, we briefly recapitulate how RNATs have been discovered in the past, before we go on to discuss the potential of recently established next-generation sequencing techniques for genome-wide identification of new regulatory RNA elements.

Katherine E DeiganAdrian R. In vivo global structure probing strategies have been attempted only very recently and applied to A. Bacterial riboswitches and RNA thermometers: You can login by using one of your existing accounts.

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Bacterial RNA thermometers: molecular zippers and switches – Wikidata

Structural data can be used to constrain RNA zippdrs prediction algorithms in order to obtain thermometes accurate experimentally-derived secondary structure models of all the sequenced transcripts. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Structured RNA elements are known to respond to different stimuli, for example metabolite-sensing riboswitches Serganov and Nudler, 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.

The prfA thermosensor is peculiar as it integrates rha only the temperature signal by structural changes but also metabolic information via a riboswitch-derived small regulatory RNA Loh et al. Increasing or decreasing temperatures alter the conformation of that structure, allowing or preventing ribosome access and thus translation. RNA Search for additional papers on this topic. Therefore, unbiased experimental high-throughput approaches are desirable for the identification of regulatory RNA structures on a global scale.

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.

The first reported RNAT are unique and rather complex. Sangita Phadtare RNA biology 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 growing awareness of temperature-responsive RNA structures triggered systematic searches for RNATs upstream of heat shock and virulence genes. Such global RNA folding profiles allow the identification of structural features involved in RNA-related processes, such as translation regulation, splicing and microRNA-mediated regulation.