RNA thermometer
Encyclopedia
An RNA thermometer 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 implicated in other regulatory roles such as in pathogenicity
and starvation
.
In general, RNA thermometers operate by changing their secondary structure
in response to temperature fluctuations. This structural transition can then expose or occlude important regions of RNA such as a ribosome binding site, which then affects the translation
rate of a nearby protein-coding gene
.
RNA thermometers, along with riboswitches, are used as examples in support of the RNA world hypothesis
. This theory proposes that RNA was once the sole nucleic acid
present in cells, and was replaced by the current DNA → RNA → protein
system.
Examples of RNA thermometers include FourU
, the Hsp90 cis-regulatory element
and the ROSE element
.
cIII mRNA were found to affect the level of translation of the cIII protein. This protein is involved in selection of either a lytic
or lysogenic life cycle in λ phage, with high concentrations of cIII promoting lysogeny. Further study of this upstream RNA region identified two alternative secondary structure
s; experimental study found the structures to be interchangeable, and dependent on both magnesium ion
concentration and temperature. This RNA thermometer is now thought to encourage entry to a lytic cycle under heat stress in order for the bacteriophage
to rapidly replicate and escape the host cell.
The term "RNA thermometer" was not coined until 1999, when it was applied to the rpoH RNA element identified in Escherichia coli
. More recently, bioinformatics
searches have been employed to uncover several novel candidate RNA thermometers. Traditional sequence-based searches are inefficient, however, as the secondary structure of the element is much more conserved
than the nucleic acid sequence.
s—though it has been suggested this fact may be due, in part, to sampling bias and inherent difficulties of detecting short, unconserved RNA sequences in genomic data
.
Though predominantly found in prokaryote
s, a potential RNA thermometer has been found in mammal
s including human
s. The candidate thermosensor heat shock RNA-1 (HSR1) activates heat-shock transcription factor 1
(HSF1) and induces protective proteins when cell temperature exceeds 37°C (body temperature
), thus preventing the cells from overheating.
s and is found in the mRNA of a heat-shock protein, hsp17, in Synechocystis
species PCC 6803. Generally these RNA elements range in length from 60-110 nucleotides and they typically contain a hairpin
with a small number of mismatched base pairs which reduce the stability of the structure, thereby allowing easier unfolding in response to a temperature increase.
Detailed structural analysis of the ROSE RNA thermometer revealed that the mismatched bases are actually engaged in nonstandard basepairing that preserves the helical structure of the RNA (see figure). The unusual basepairs consist of G-G, U-U, and UC-U pairs. Since these noncanonical base pairs are relatively unstable, increased temperature causes local melting of the RNA structure in this region, exposing the Shine-Dalgarno sequence.
Some RNA thermometers are significantly more complex than a single hairpin, as in the case of a region found in CspA mRNA
which is thought to contain a pseudoknot
, as well as multiple hairpins.
Synthetic
RNA thermometers have been designed with just a simple single-hairpin structure. However, the primary sequence of such short RNA thermometers can be sensitive to mutation, as a single base change
can render the hairpin inactive in vivo
.
UTR of messenger RNA, upstream of a protein-coding gene. Here they are able to occlude the ribosome binding site (RBS) and prevent translation of the mRNA into protein. As temperature increases, the hairpin structure can 'melt' and expose the RBS or Shine-Dalgarno sequence
to permit binding of the small ribosomal subunit (30S
), which then assembles other translation machinery. The start codon
, typically found 8 nucleotides downstream of the Shine-Dalgarno sequence, signals the beginning of a protein-coding gene which is then translated to a peptide
product by the ribosome
. In addition to this cis-acting
mechanism, a lone example of a trans-acting
RNA thermometer has been found in RpoS mRNA
where it is thought to be involved in the starvation response.
A specific example of an RNA thermometer motif is the FourU thermometer found in Salmonella enterica
. When exposed to temperatures above 45°C, the stem-loop
that base-pairs opposite the Shine-Dalgarno sequence becomes unpaired and allows the mRNA to enter the ribosome for translation to occur. Mg2+
ion concentration has also been shown to affect the stability of FourU. The most well-studied RNA thermometer is found in the rpoH gene in Escherichia coli. This thermosensor upregulates heat shock proteins under high temperatures through σ32, a specialised heat-shock sigma factor
.
Though typically associated with heat-induced protein expression, RNA thermometers can also regulate cold-shock proteins. For example, the expression of two 7kDa
proteins are regulated by an RNA thermometer in the thermophilic
bacterium Thermus thermophilus
and a similar mechanism has been identified in Enterobacteriales.
RNA thermometers sensitive to temperatures of 37°C can be used by pathogen
s to activate infection-specific genes. For example, the upregulation
of prfA, encoding a key transcriptional regulator of virulence
genes in Listeria monocytogenes, was demonstrated by fusing the 5' DNA of prfA
to the green fluorescent protein
gene; the gene fusion was then transcribed from the T7 promoter in E. coli, and fluorescence was observed at 37°C but not at 30°C.
, with different sequences acting as biocatalysts, regulators and sensors. The hypothesis then proposes that modern DNA, RNA and protein-based life
evolved and selection
replaced the majority of RNA's roles with other biomolecule
s.
RNA thermometers and riboswitches are thought to be evolutionarily ancient
due to their wide-scale distribution in distantly-related organisms. It has been proposed that, in the RNA world, RNA thermosensors would have been responsible for temperature-dependent regulation of other RNA molecules. RNA thermometers in modern organisms may be molecular fossils
which could hint at a previously more widespread importance in an RNA world.
Temperature
Temperature is a physical property of matter that quantitatively expresses the common notions of hot and cold. Objects of low temperature are cold, while various degrees of higher temperatures are referred to as warm or hot...
-sensitive non-coding RNA
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
molecule which regulates gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
. RNA thermometers often regulate genes required during either a heat shock
Heat shock
In biochemistry, heat shock is the effect of subjecting a cell to a higher temperature than that of the ideal body temperature of the organism from which the cell line was derived.-Heat shock response:...
or cold shock
Cold shock response
Cold shock response is the physiological response of organisms to sudden cold, especially cold water.-Myth of sudden hypothermia:In humans, cold shock response is perhaps the most common cause of death from immersion in very cold water, such as by falling through thin ice...
response, but have been implicated in other regulatory roles such as in pathogenicity
Pathogenicity
Pathogenicity is the ability of a pathogen to produce an infectious disease in an organism.It is often used interchangeably with the term "virulence", although virulence is used more specifically to describe the relative degree of damage done by a pathogen, or the degree of pathogenicity caused by...
and starvation
Starvation
Starvation is a severe deficiency in caloric energy, nutrient and vitamin intake. It is the most extreme form of malnutrition. In humans, prolonged starvation can cause permanent organ damage and eventually, death...
.
In general, RNA thermometers operate by changing their secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
in response to temperature fluctuations. This structural transition can then expose or occlude important regions of RNA such as a ribosome binding site, which then affects the translation
Prokaryotic translation
Prokaryotic translation is the process by which messenger RNA is translated into proteins in prokaryotes.-Initiation:Initiation of translation in prokaryotes involves the assembly of the components of the translation system which are: the two ribosomal subunits , the mRNA to be translated, the...
rate of a nearby protein-coding gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
.
RNA thermometers, along with riboswitches, are used as examples in support of the RNA world hypothesis
RNA world hypothesis
The RNA world hypothesis proposes that life based on ribonucleic acid pre-dates the current world of life based on deoxyribonucleic acid , RNA and proteins. RNA is able both to store genetic information, like DNA, and to catalyze chemical reactions, like an enzyme protein...
. This theory proposes that RNA was once the sole nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
present in cells, and was replaced by the current DNA → RNA → protein
Central dogma of molecular biology
The central dogma of molecular biology was first articulated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:In other words, the process of producing proteins is irreversible: a protein cannot be used to create DNA....
system.
Examples of RNA thermometers include FourU
FourU thermometer
FourU thermometers are a class of non-coding RNA thermometers found in Salmonella. They are named 'FourU' due to the four highly conserved uridine nucleotides found directly opposite the Shine-Dalgarno sequence on hairpin II ....
, the Hsp90 cis-regulatory element
Hsp90 cis-regulatory element
The Hsp90 cis regulatory element is an RNA element found in the 5' UTR of the Drosophila hsp90 mRNA. It is required for increased translational efficiency during the heat shock response....
and the ROSE element
Repression of heat shock gene expression (ROSE) element
The repression of heat shock gene expression 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 structure is thought to be altered by temperature, thus it is an...
.
Discovery
The first temperature-sensitive RNA element was reported in 1989. Prior to this research, mutations upstream from the transcription start site in a lambda (λ) phageLambda phage
Enterobacteria phage λ is a temperate bacteriophage that infects Escherichia coli.Lambda phage is a virus particle consisting of a head, containing double-stranded linear DNA as its genetic material, and a tail that can have tail fibers. The phage particle recognizes and binds to its host, E...
cIII mRNA were found to affect the level of translation of the cIII protein. This protein is involved in selection of either a lytic
Lytic cycle
The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle is typically considered the main method of viral replication, since it results in the destruction of the infected cell...
or lysogenic life cycle in λ phage, with high concentrations of cIII promoting lysogeny. Further study of this upstream RNA region identified two alternative secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
s; experimental study found the structures to be interchangeable, and dependent on both magnesium ion
Magnesium in biology
Magnesium is an essential element in biological systems. Magnesium occurs typically as the Mg2+ ion. It is an essential mineral nutrient for life and is present in every cell type in every organism. For example, ATP , the main source of energy in cells, must be bound to a magnesium ion in order to...
concentration and temperature. This RNA thermometer is now thought to encourage entry to a lytic cycle under heat stress in order for the bacteriophage
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
to rapidly replicate and escape the host cell.
The term "RNA thermometer" was not coined until 1999, when it was applied to the rpoH RNA element identified in Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
. More recently, bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
searches have been employed to uncover several novel candidate RNA thermometers. Traditional sequence-based searches are inefficient, however, as the secondary structure of the element is much more conserved
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...
than the nucleic acid sequence.
Distribution
Most known RNA thermometers are located in the 5' untranslated region (UTR) of messenger RNA encoding heat shock proteinHeat shock protein
Heat shock proteins are a class of functionally related proteins involved in the folding and unfolding of other proteins. Their expression is increased when cells are exposed to elevated temperatures or other stress. This increase in expression is transcriptionally regulated...
s—though it has been suggested this fact may be due, in part, to sampling bias and inherent difficulties of detecting short, unconserved RNA sequences in genomic data
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
.
Though predominantly found in prokaryote
Prokaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...
s, a potential RNA thermometer has been found in mammal
Mammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...
s including human
Human
Humans are the only living species in the Homo genus...
s. The candidate thermosensor heat shock RNA-1 (HSR1) activates heat-shock transcription factor 1
HSF1
Heat shock factor protein 1 is a protein that in humans is encoded by the HSF1 gene.-Function:The product of this gene is a heat-shock transcription factor. Transcription of heat-shock genes is rapidly induced after temperature stress...
(HSF1) and induces protective proteins when cell temperature exceeds 37°C (body temperature
Normal human body temperature
Normal human body temperature, also known as normothermia or euthermia, is a concept that depends upon the place in the body at which the measurement is made, and the time of day and level of activity of the person...
), thus preventing the cells from overheating.
Structure
RNA thermometers are structurally simple and can be made from short RNA sequences; the smallest is just 44 nucleotideNucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s and is found in the mRNA of a heat-shock protein, hsp17, in Synechocystis
Synechocystis
Synechocystis sp. PCC6803 is a freshwater cyanobacterium capable of both phototrophic growth by oxygenic photosynthesis in sunlight and heterotrophic growth by glycolysis and oxidative phosphorylation during dark periods...
species PCC 6803. Generally these RNA elements range in length from 60-110 nucleotides and they typically contain a hairpin
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
with a small number of mismatched base pairs which reduce the stability of the structure, thereby allowing easier unfolding in response to a temperature increase.
Detailed structural analysis of the ROSE RNA thermometer revealed that the mismatched bases are actually engaged in nonstandard basepairing that preserves the helical structure of the RNA (see figure). The unusual basepairs consist of G-G, U-U, and UC-U pairs. Since these noncanonical base pairs are relatively unstable, increased temperature causes local melting of the RNA structure in this region, exposing the Shine-Dalgarno sequence.
Some RNA thermometers are significantly more complex than a single hairpin, as in the case of a region found in CspA mRNA
CspA mRNA 5' UTR
cspA mRNA 5' UTR is the untranslated region of the , which is important in the cold shock response in Enterobacteriales such as E. coli. The 5' UTR element acts as an RNA thermometer, regulating the expression of cspA in response to temperature....
which is thought to contain a pseudoknot
Pseudoknot
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982...
, as well as multiple hairpins.
Synthetic
Synthetic biology
Synthetic biology is a new area of biological research that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions...
RNA thermometers have been designed with just a simple single-hairpin structure. However, the primary sequence of such short RNA thermometers can be sensitive to mutation, as a single base change
Point mutation
A point mutation, or single base substitution, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material, DNA or RNA. Often the term point mutation also includes insertions or deletions of a single base pair...
can render the hairpin inactive in vivo
In vivo
In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...
.
Mechanism
RNA thermometers are found in the 5'Directionality (molecular biology)
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 5′-end and a 3′-end...
UTR of messenger RNA, upstream of a protein-coding gene. Here they are able to occlude the ribosome binding site (RBS) and prevent translation of the mRNA into protein. As temperature increases, the hairpin structure can 'melt' and expose the RBS or Shine-Dalgarno sequence
Shine-Dalgarno sequence
The Shine-Dalgarno sequence , proposed by Australian scientists John Shine and Lynn Dalgarno , is a ribosomal binding site in the mRNA, generally located 8 basepairs upstream of the start codon AUG. The Shine-Dalgarno sequence exists only in prokaryotes. The six-base consensus sequence is AGGAGG;...
to permit binding of the small ribosomal subunit (30S
30S
30S is the smaller subunit of the 70S ribosome of prokaryotes. It is a complex of ribosomal RNA and ribonucleoproteins that functions in mRNA translation...
), which then assembles other translation machinery. The start codon
Start codon
The start codon is generally defined as the point, sequence, at which a ribosome begins to translate a sequence of RNA into amino acids.When an RNA transcript is "read" from the 5' carbon to the 3' carbon by the ribosome the start codon is the first codon on which the tRNA bound to Met,...
, typically found 8 nucleotides downstream of the Shine-Dalgarno sequence, signals the beginning of a protein-coding gene which is then translated to a peptide
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...
product by the ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
. In addition to this cis-acting
Cis-regulatory element
A cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA . This term is constructed from the Latin word cis, which means "on the same side as". These cis-regulatory elements are often binding sites for one or...
mechanism, a lone example of a trans-acting
Trans-acting
In the field of molecular biology, trans-acting , in general, means "acting from a different molecule"...
RNA thermometer has been found in RpoS mRNA
RpoS mRNA 5'UTR
rpoS mRNA encodes for the rpoS stress factor, sigma E , where DsrA in conjunction with the Sm like RNA binding protein, Hfq promote the translation of this rpoS mRNA. The 5' UTR of the rpoS mRNA forms a self inhibitory stem loop that shields the shine-dalgarno sequence and therefore inhibits...
where it is thought to be involved in the starvation response.
A specific example of an RNA thermometer motif is the FourU thermometer found in Salmonella enterica
Salmonella enterica
Salmonella enterica is a rod-shaped flagellated, facultative anaerobic, Gram-negative bacterium, and a member of the genus Salmonella.- Epidemiology :...
. When exposed to temperatures above 45°C, the stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
that base-pairs opposite the Shine-Dalgarno sequence becomes unpaired and allows the mRNA to enter the ribosome for translation to occur. Mg2+
Magnesium
Magnesium is a chemical element with the symbol Mg, atomic number 12, and common oxidation number +2. It is an alkaline earth metal and the eighth most abundant element in the Earth's crust and ninth in the known universe as a whole...
ion concentration has also been shown to affect the stability of FourU. The most well-studied RNA thermometer is found in the rpoH gene in Escherichia coli. This thermosensor upregulates heat shock proteins under high temperatures through σ32, a specialised heat-shock sigma factor
Sigma factor
A sigma factor is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. Different sigma factors are activated in response to different environmental conditions...
.
Though typically associated with heat-induced protein expression, RNA thermometers can also regulate cold-shock proteins. For example, the expression of two 7kDa
Atomic mass unit
The unified atomic mass unit or dalton is a unit that is used for indicating mass on an atomic or molecular scale. It is defined as one twelfth of the rest mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state, and has a value of...
proteins are regulated by an RNA thermometer in the thermophilic
Thermophile
A thermophile is an organism — a type of extremophile — that thrives at relatively high temperatures, between 45 and 122 °C . Many thermophiles are archaea...
bacterium Thermus thermophilus
Thermus thermophilus
Thermus thermophilus is a Gram negative eubacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely thermophilic, with an optimal growth temperature of about...
and a similar mechanism has been identified in Enterobacteriales.
RNA thermometers sensitive to temperatures of 37°C can be used by pathogen
Pathogen
A pathogen gignomai "I give birth to") or infectious agent — colloquially, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host...
s to activate infection-specific genes. For example, the upregulation
Downregulation and upregulation
Downregulation is the process by which a cell decreases the quantity of a cellular component, such as RNA or protein, in response to an external variable...
of prfA, encoding a key transcriptional regulator of virulence
Virulence
Virulence is by MeSH definition the degree of pathogenicity within a group or species of parasites as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenicity of an organism - its ability to cause disease - is determined by its...
genes in Listeria monocytogenes, was demonstrated by fusing the 5' DNA of prfA
PrfA thermoregulator UTR
The PrfA thermoregulator UTR is an RNA thermometer found in the 5' UTR of the prfA gene. In Listeria monocytogenes, virulence genes are maximally expressed at 37°C but are almost silent at 30°C. The genes are controlled by PrfA, a transcriptional activator whose expression is thermoregulated...
to the green fluorescent protein
Green fluorescent protein
The green fluorescent protein is a protein composed of 238 amino acid residues that exhibits bright green fluorescence when exposed to blue light. Although many other marine organisms have similar green fluorescent proteins, GFP traditionally refers to the protein first isolated from the...
gene; the gene fusion was then transcribed from the T7 promoter in E. coli, and fluorescence was observed at 37°C but not at 30°C.
Implications for the RNA world hypothesis
The RNA world hypothesis states that RNA was once both the carrier of hereditary information and enzymatically activeEnzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
, with different sequences acting as biocatalysts, regulators and sensors. The hypothesis then proposes that modern DNA, RNA and protein-based life
Central dogma of molecular biology
The central dogma of molecular biology was first articulated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:In other words, the process of producing proteins is irreversible: a protein cannot be used to create DNA....
evolved and selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
replaced the majority of RNA's roles with other biomolecule
Biomolecule
A biomolecule is any molecule that is produced by a living organism, including large polymeric molecules such as proteins, polysaccharides, lipids, and nucleic acids as well as small molecules such as primary metabolites, secondary metabolites, and natural products...
s.
RNA thermometers and riboswitches are thought to be evolutionarily ancient
Timeline of evolution
This timeline of evolution of life outlines the major events in the development of life on planet Earth since it first originated until the present day. In biology, evolution is any change across successive generations in the heritable characteristics of biological populations...
due to their wide-scale distribution in distantly-related organisms. It has been proposed that, in the RNA world, RNA thermosensors would have been responsible for temperature-dependent regulation of other RNA molecules. RNA thermometers in modern organisms may be molecular fossils
Living fossil
Living fossil is an informal term for any living species which appears similar to a species otherwise only known from fossils and which has no close living relatives, or a group of organisms which have long fossil records...
which could hint at a previously more widespread importance in an RNA world.
Other examples
- Hsp90 cis-regulatory elementHsp90 cis-regulatory elementThe Hsp90 cis regulatory element is an RNA element found in the 5' UTR of the Drosophila hsp90 mRNA. It is required for increased translational efficiency during the heat shock response....
regulates hsp90Hsp90Hsp90 is a molecular chaperone and is one of the most abundant proteins expressed in cells. It is a member of the heat shock protein family, which is upregulated in response to stress...
in DrosophilaDrosophilaDrosophila is a genus of small flies, belonging to the family Drosophilidae, whose members are often called "fruit flies" or more appropriately pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many species to linger around overripe or rotting fruit...
, increasing the translation rate of the heat shock protein at high temperatures. - The ibpAB operonOperonIn genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo trans-splicing to create...
of E. coli is predicted to contain two co-operative RNA thermometers: a ROSE elementRepression of heat shock gene expression (ROSE) elementThe repression of heat shock gene expression 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 structure is thought to be altered by temperature, thus it is an...
and the IbpB thermometerIbpB thermometerThe IbpB thermometer is an RNA thermometer element found in the ibpAB operon. The operon contains two heat-shock genes, encoding inclusion body binding proteins A and B , and is the most drastically upregulated operon under heat-shock in Escherichia coli.IbpA is regulated by a ROSE element found in...
. - ROSE1 and ROSEAT2 are found in rhizobialesRhizobialesRhizobiales is an order of alpha proteobacteria. They are gram-negative.The rhizobia, which fix nitrogen and are symbiotic with plant roots, appear in several different families here. The Bradyrhizobiaceae, Hyphomicrobiaceae, Phyllobacteriaceae, and Rhizobiaceae are the four families that contain...
Bradyrhizobium japonicumBradyrhizobium japonicumBradyrhizobium japonicum is a species of legume-root nodulating, microsymbiotic nitrogen-fixing bacterium species. B. japonicum is identified as a DNA homology group .B...
and Agrobacterium tumefaciensAgrobacterium tumefaciensAgrobacterium tumefaciens is the causal agent of crown gall disease in over 140 species of dicot. It is a rod shaped, Gram negative soil bacterium...
respectively. They exist in the 5' UTR of HspA mRNA, and repress heat shock protein translation at physiological temperatures.