FourU thermometer

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{{Infobox rfam

| Name = FourU

| image = FourU.png

| width = 226px

| caption = Consensus secondary structure of FourU RNA thermometers. Red colouring indicates the highest levels of nucleotide conservation.

| Symbol = FourU

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| Rfam = RF01795

| RNA_type = RNA thermometer

| Tax_domain = Salmonella;

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FourU thermometers are a class of non-coding RNA thermometers found in Salmonella.{{cite journal | vauthors = Waldminghaus T, Heidrich N, Brantl S, Narberhaus F | title = FourU: a novel type of RNA thermometer in Salmonella | journal = Molecular Microbiology | volume = 65 | issue = 2 | pages = 413–424 | date = July 2007 | pmid = 17630972 | doi = 10.1111/j.1365-2958.2007.05794.x | doi-access = free }} They are named 'FourU' due to the four highly conserved uridine nucleotides found directly opposite the Shine-Dalgarno sequence on hairpin II (pictured).

RNA thermometers such as FourU control regulation of temperature via heat shock proteins in many prokaryotes.{{cite journal | vauthors = Rinnenthal J, Klinkert B, Narberhaus F, Schwalbe H | title = Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution | journal = Nucleic Acids Research | volume = 38 | issue = 11 | pages = 3834–3847 | date = June 2010 | pmid = 20211842 | pmc = 2887971 | doi = 10.1093/nar/gkq124 }}{{cite journal | vauthors = Narberhaus F, Waldminghaus T, Chowdhury S | title = RNA thermometers | journal = FEMS Microbiology Reviews | volume = 30 | issue = 1 | pages = 3–16 | date = January 2006 | pmid = 16438677 | doi = 10.1111/j.1574-6976.2005.004.x | doi-access = }}{{cite journal | vauthors = Waldminghaus T, Fippinger A, Alfsmann J, Narberhaus F | title = RNA thermometers are common in alpha- and gamma-proteobacteria | journal = Biological Chemistry | volume = 386 | issue = 12 | pages = 1279–1286 | date = December 2005 | pmid = 16336122 | doi = 10.1515/BC.2005.145 | s2cid = 84557068 }} FourU thermometers are relatively small RNA molecules, only 57 nucleotides in length, and have a simple two-hairpin structure.

FourU are found in the 5' untranslated region of the gene for heat shock protein Salmonella agsA,{{cite web |url=https://www.ncbi.nlm.nih.gov/protein/267850646 |title=aggregation suppressing protein |publisher=National Center for Biotechnology Information}}{{cite journal | vauthors = Tomoyasu T, Takaya A, Sasaki T, Nagase T, Kikuno R, Morioka M, Yamamoto T | title = A new heat shock gene, AgsA, which encodes a small chaperone involved in suppressing protein aggregation in Salmonella enterica serovar typhimurium | journal = Journal of Bacteriology | volume = 185 | issue = 21 | pages = 6331–6339 | date = November 2003 | pmid = 14563868 | pmc = 219406 | doi = 10.1128/JB.185.21.6331-6339.2003 }} they repress translation of this protein by base-pairing the Shine-Dalgarno sequence of the gene's mRNA. This prevents ribosomes from binding the start codon of the gene.{{cite journal | vauthors = Shine J, Dalgarno L |author1-link=John Shine |author2-link=Lynn Dalgarno| title = Determinant of cistron specificity in bacterial ribosomes | journal = Nature | volume = 254 | issue = 5495 | pages = 34–38 | date = March 1975 | pmid = 803646 | doi = 10.1038/254034a0 | s2cid = 4162567 }}

They are also found in the 5'UTR of htrA (high temperature requirement) genes in Salmonella and E.coli.{{cite journal | vauthors = Klinkert B, Cimdins A, Gaubig LC, Roßmanith J, Aschke-Sonnenborn U, Narberhaus F | title = Thermogenetic tools to monitor temperature-dependent gene expression in bacteria | journal = Journal of Biotechnology | volume = 160 | issue = 1–2 | pages = 55–63 | date = July 2012 | pmid = 22285954 | doi = 10.1016/j.jbiotec.2012.01.007 }}

In V. cholerae fourU thermometer in the 5' of toxT controls its temperature-dependent translation. At human body temperature, the thermometer structure opens and to allow transcriptional activator protein ToxT translation, facilitating V. cholerae virulence.{{cite journal | vauthors = Weber GG, Kortmann J, Narberhaus F, Klose KE | title = RNA thermometer controls temperature-dependent virulence factor expression in Vibrio cholerae | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 39 | pages = 14241–14246 | date = September 2014 | pmid = 25228776 | pmc = 4191814 | doi = 10.1073/pnas.1411570111 | doi-access = free }}

Other known RNA thermometers include the ROSE element{{cite journal | vauthors = Nocker A, Hausherr T, Balsiger S, Krstulovic NP, Hennecke H, Narberhaus F | title = A mRNA-based thermosensor controls expression of rhizobial heat shock genes | journal = Nucleic Acids Research | volume = 29 | issue = 23 | pages = 4800–4807 | date = December 2001 | pmid = 11726689 | pmc = 96696 | doi = 10.1093/nar/29.23.4800 }}{{cite journal | vauthors = Waldminghaus T, Gaubig LC, Narberhaus F | title = Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers | journal = Molecular Genetics and Genomics | volume = 278 | issue = 5 | pages = 555–564 | date = November 2007 | pmid = 17647020 | doi = 10.1007/s00438-007-0272-7 | s2cid = 24747327 }} and Hsp90 cis-reg element.{{cite journal | vauthors = Ahmed R, Duncan RF | title = Translational regulation of Hsp90 mRNA. AUG-proximal 5'-untranslated region elements essential for preferential heat shock translation | journal = The Journal of Biological Chemistry | volume = 279 | issue = 48 | pages = 49919–49930 | date = November 2004 | pmid = 15347681 | doi = 10.1074/jbc.M404681200 | doi-access = free }}

Response to temperature

Hairpin II appears to be a dynamic feature of FourU's secondary structure. It undergoes a conformational shift when exposed to temperatures above 45 °C, becoming increasingly unpaired as temperature rises. Hairpin I, in contrast, remains stably base-paired in temperatures as high as 50 °C, which implies the structural shift of hairpin II from closed to open may have an important role in heat shock response. A later study used mutant analysis and calculations of enthalpy and entropy to support a cooperative zipper-type unfolding mechanism of FourU hairpin II in response to temperature increase.

Sigma factor cooperation

Like other RNA thermometers, FourU is not solely responsible for temperature-dependent expression of its adjacent gene.{{cite journal | vauthors = Johansson J, Mandin P, Renzoni A, Chiaruttini C, Springer M, Cossart P | title = An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes | journal = Cell | volume = 110 | issue = 5 | pages = 551–561 | date = September 2002 | pmid = 12230973 | doi = 10.1016/S0092-8674(02)00905-4 | doi-access = free }} Instead, it operates in conjunction with a sigma factor (σ³²){{cite journal | vauthors = Bukau B | title = Regulation of the Escherichia coli heat-shock response | journal = Molecular Microbiology | volume = 9 | issue = 4 | pages = 671–680 | date = August 1993 | pmid = 7901731 | doi = 10.1111/j.1365-2958.1993.tb01727.x | s2cid = 39147026 }} which is known to also regulate many other genes.{{cite journal | vauthors = Permina EA, Gelfand MS | title = Heat shock (sigma32 and HrcA/CIRCE) regulons in beta-, gamma- and epsilon-proteobacteria | journal = Journal of Molecular Microbiology and Biotechnology | volume = 6 | issue = 3–4 | pages = 174–181 | year = 2003 | pmid = 15153770 | doi = 10.1159/000077248 | s2cid = 84915084 }} Sigma factor-RNA thermometer combinations have been found to regulate other heat-shock genes (such as ibpA in E. coli) which has led to speculation{{By whom|date=April 2011}} of undiscovered RNA thermometers operating alongside sigma factor modules to regulate other related genes as an additional level of control. Further speculation suggests the simpler RNA thermometer method of gene regulation may have evolved prior to the more complex sigma factor transcription control.

agsA function

The agsA gene, which is regulated by FourU thermometers, was first discovered in Salmonella enterica. The protein coded for by this gene is a small heat shock protein (sHSP) which protects bacteria from irreversible aggregation of proteins and aids in their refolding. Mutant analysis confirmed the importance of agsA: a plasmid containing the gene and a promoter increased the survival rate of a thermosenstive mutant phenotype by remedying protein aggregation at high temperatures. It has a similar function to the human chaperone α-crystallin.{{cite journal | vauthors = Rajaraman K, Raman B, Ramakrishna T, Rao CM | title = Interaction of human recombinant alphaA- and alphaB-crystallins with early and late unfolding intermediates of citrate synthase on its thermal denaturation | journal = FEBS Letters | volume = 497 | issue = 2–3 | pages = 118–123 | date = May 2001 | pmid = 11377425 | doi = 10.1016/S0014-5793(01)02451-6 | doi-access = }}

References

External links

{{Rfam|id=RF01795|name=FourU thermometer RNA element}}

Category:Non-coding RNA

Category:Cis-regulatory RNA elements