__NOTOC__ FourU thermometers are a class of

non-coding RNA A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non- ...

thermometers found in ''

Salmonella ''Salmonella'' is a genus of rod-shaped (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two species of ''Salmonella'' are ''Salmonella enterica'' and '' Salmonella bongori''. ''S. enterica'' is the type species and is fur ...

''. They are named 'FourU' due to the four highly conserved

uridine Uridine (symbol U or Urd) is a glycosylated pyrimidine analog containing uracil attached to a ribose ring (or more specifically, a ribofuranose) via a β-N1-glycosidic bond. The analog is one of the five standard nucleosides which make up nucl ...

nucleotides found directly opposite the Shine-Dalgarno sequence on hairpin II (''pictured'').

RNA thermometer An RNA thermometer (or RNA thermosensor) is a temperature-sensitive non-coding RNA molecule which regulates gene expression. RNA thermometers often regulate genes required during either a heat shock or cold shock response, but have been impli ...

s such as FourU control regulation of

temperature Temperature is a physical quantity that expresses quantitatively the perceptions of hotness and coldness. Temperature is measured with a thermometer. Thermometers are calibrated in various temperature scales that historically have relied on ...

via

heat shock proteins Heat shock proteins (HSP) are a family of proteins produced by cells in response to exposure to stressful conditions. They were first described in relation to heat shock, but are now known to also be expressed during other stresses including exp ...

in many

prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...

s. FourU thermometers are relatively small RNA molecules, only 57

nucleotides Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...

in length, and have a simple two-

hairpin A hairpin or hair pin is a long device used to hold a person's hair in place. It may be used simply to secure long hair out of the way for convenience or as part of an elaborate hairstyle or coiffure. The earliest evidence for dressing the hai ...

structure. FourU are found in the

5' untranslated region The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly upstream from the initiation codon. This region is important for the regulation of t ...

of the

gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

for heat shock protein ''Salmonella agsA'', they repress

translation Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...

of this protein by

base-pairing A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...

the Shine-Dalgarno sequence of the gene's

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...

. This prevents ribosomes from binding the start codon of the gene. They are also found in the 5'UTR of ''htrA'' (high temperature requirement) genes in ''Salmonella'' and ''E.coli.'' 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. Other known RNA thermometers include the

ROSE element The repression of heat shock gene expression (ROSE) element is an RNA element found in the 5' UTR of some heat shock protein's mRNAs. The ROSE element is an RNA thermometer that negatively regulates heat shock gene expression. The secondary s ...

and Hsp90 cis-reg element.

Response to temperature

Hairpin A hairpin or hair pin is a long device used to hold a person's hair in place. It may be used simply to secure long hair out of the way for convenience or as part of an elaborate hairstyle or coiffure. The earliest evidence for dressing the hai ...

II appears to be a dynamic feature of FourU's

secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...

. 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 The heat shock response (HSR) is a cell stress response that increases the number of molecular chaperones to combat the negative effects on proteins caused by stressors such as increased temperatures, oxidative stress, and heavy metals. In a norm ...

response. A later study used

mutant In biology, and especially in genetics, a mutant is an organism or a new genetic character arising or resulting from an instance of mutation, which is generally an alteration of the DNA sequence of the genome or chromosome of an organism. It ...

analysis and calculations of

enthalpy Enthalpy , a property of a thermodynamic system, is the sum of the system's internal energy and the product of its pressure and volume. It is a state function used in many measurements in chemical, biological, and physical systems at a constant ...

and

entropy Entropy is a scientific concept, as well as a measurable physical property, that is most commonly associated with a state of disorder, randomness, or uncertainty. The term and the concept are used in diverse fields, from classical thermodyna ...

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. Instead, it operates in conjunction with a

sigma factor A sigma factor (σ factor or specificity factor) is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is ho ...

(σ³²) which is known to also regulate many other genes. Sigma factor-RNA thermometer combinations have been found to regulate other heat-shock genes (such as ibpA in ''

E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...

'') which has led to speculation of undiscovered RNA thermometers operating alongside sigma factor modules to

regulate Regulate may refer to: * Regulation Regulation is the management of complex systems according to a set of rules and trends. In systems theory, these types of rules exist in various fields of biology Biology is the scientific study o ...

other related genes as an additional level of control. Further speculation suggests the simpler RNA thermometer method of gene regulation may have

evolved Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation te ...

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 ''Salmonella enterica'' (formerly ''Salmonella choleraesuis'') is a rod-headed, flagellate, facultative anaerobic, Gram-negative bacterium and a species of the genus '' Salmonella''. A number of its serovars are serious human pathogens. Epidem ...

''. The protein coded for by this gene is a small

heat shock protein Heat shock proteins (HSP) are a family of proteins produced by cells in response to exposure to stressful conditions. They were first described in relation to heat shock, but are now known to also be expressed during other stresses including exp ...

(sHSP) which protects

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

from irreversible

aggregation Aggregation may refer to: Business and economics * Aggregation problem (economics) * Purchasing aggregation, the joining of multiple purchasers in a group purchasing organization to increase their buying power * Community Choice Aggregation, the ...

of proteins and aids in their refolding. Mutant analysis confirmed the importance of agsA: a

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; howev ...

containing the gene and a promoter increased the survival rate of a thermosenstive mutant

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological prop ...

by remedying protein aggregation at high temperatures. It has a similar function to the human chaperone α-crystallin.

References

External links

* {{Rfam, id=RF01795, name=FourU thermometer RNA element Non-coding RNA Cis-regulatory RNA elements

Response to temperature

Sigma factor cooperation

agsA function

See also

References

Further reading

External links