RNA thermometers

Narberhaus, Franz; Waldminghaus, Torsten; Chowdhury, Saheli

doi:10.1111/j.1574-6976.2005.004.x

Cited by 266 publications

(228 citation statements)

References 103 publications

(145 reference statements)

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“…Riboswitches [5][6][7] beautifully illustrate how complex RNA dynamics can be used to achieve highly tunable and adaptable biological regulation (Figure 1b). Riboswitches are cis-acting mRNA elements that allow cells to adaptively change gene expression in response to their changing environment.…”

Section: Riboswitchesmentioning

confidence: 99%

RNA dynamics: it is about time

Al‐Hashimi

Walter

2008

Current Opinion in Structural Biology

298

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SummaryMany recently discovered RNA functions rely on highly complex multi-step conformational transitions that occur in response to an array of cellular signals. These dynamics accompany and guide, for example, RNA co-transcriptional folding, ligand sensing and signaling, site-specific catalysis in ribozymes, and the hierarchically ordered assembly of ribonucleoproteins. RNA dynamics are encoded by both the inherent properties of RNA structure, spanning many motional modes with a large range of amplitudes and timescales, and external trigger factors, ranging from proteins, nucleic acids, metal ions, metabolites, and vitamins to temperature and even directional RNA biosynthesis itself. Here, we review recent advances in our understanding of RNA dynamics as highlighted by biophysical tools.

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Section: Riboswitchesmentioning

confidence: 99%

RNA dynamics: it is about time

Al‐Hashimi

Walter

2008

Current Opinion in Structural Biology

298

295

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“…The translation of rpoH is under the regulation of a cisacting RNA element located in the coding sequence of the rpoH gene. At low temperatures, this thermo-regulator folds into a secondary structure which overlaps and sequesters the ribosome-binding site (RBS), inhibiting rpoH translation (Narberhaus et al, 2006) (Fig. 1e).…”

Section: Rna and Rna-binding Proteins Are Important Factors Involved mentioning

confidence: 99%

New insights into the regulatory networks of paralogous genes in bacteria

et al. 2010

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Extensive genomic studies on gene duplication in model organisms such as Escherichia coli and Saccharomyces cerevisiae have recently been undertaken. In these models, it is commonly considered that a duplication event may include a transcription factor (TF), a target gene, or both. Following a gene duplication episode, varying scenarios have been postulated to describe the evolution of the regulatory network. However, in most of these, the TFs have emerged as the most important and in some cases the only factor shaping the regulatory network as the organism responds to a natural selection process, in order to fulfil its metabolic needs. Recent findings concerning the regulatory role played by elements other than TFs have indicated the need to reassess these early models. Thus, we performed an exhaustive review of paralogous gene regulation in E. coli and Bacillus subtilis based on published information, available in the NCBI PubMed database and in well-established regulatory databases. Our survey reinforces the notion that despite TFs being the most prominent components shaping the regulatory networks, other elements are also important. These include small RNAs, riboswitches, RNA-binding proteins, sigma factors, protein-protein interactions and DNA supercoiling, which modulate the expression of genes involved in particular metabolic processes or induce a more complex response in terms of the regulatory networks of paralogous genes in an integrated interplay with TFs. IntroductionGene duplication is one of the main sources of functional divergence in organisms (Babu et al., 2004;Conant & Wolfe, 2008;Gelfand, 2006;Lynch & Conery, 2000;Teichmann & Babu, 2004). In order to fulfil an organism's metabolic needs, selection processes modify the regulation of the paralogous gene copies, taking advantage of a repertoire of new functions. Duplication events may include genes coding for transcription factors (TFs), permitting a more versatile adaptation of the functional diversity gained from the duplication of structural genes. Different aspects of the evolution of the regulatory networks of paralogous genes have been examined, including the co-evolution of the upstream regulatory regions and their corresponding TFs; the likely consequences of gain, loss, and replacement of TFs in the regulatory networks of paralogous genes (Gelfand, 2006;Teichmann & Babu, 2004); and also the topological and dynamic properties of the regulatory networks (Babu et al., 2006;Balaji et al., 2007; Luscombe et al., 2004). This review will consider the fascinating repertoire of additional mechanisms other than TFs, which help regulate the expression of paralogous genes in Escherichia coli and Bacillus subtilis. This analysis is derived from an extensive compilation of the regulatory information available from the NCBI PubMed database and deposited in the E. TFs are essential elements in the regulatory networks of paralogous genes TFs are the most prominent and usually the only regulatory element taken into account in any of the aforementioned stu...

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“…RNAs have been proposed to act as cellular thermometers. 26,35,36 Certain E. coli proteins such as CspA, the main cold shock protein, and its homologs act as RNA chaperones 37,38 melting the secondary structures in nucleic acids and facilitating transcription and translation at low temperature. This activity of CspA and its homologs is essential for cold acclimation of cells.…”

Section: Rna Modulating Cold Shock Proteinsmentioning

confidence: 99%