HOME

TheInfoList



OR:

In molecular biology, a riboswitch is a regulatory segment of a
messenger RNA 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 p ...
molecule that binds a small molecule, resulting in a change in production of the
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s, catalyze reactions, or to bind other RNA or protein
macromolecule A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The ...
s. The original definition of the term "riboswitch" specified that they directly sense small-molecule
metabolite In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...
concentrations. Although this definition remains in common use, some biologists have used a broader definition that includes other cis-regulatory RNAs. However, this article will discuss only metabolite-binding riboswitches. Most known riboswitches occur in
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 ...
, but functional riboswitches of one type (the TPP riboswitch) have been discovered in archaea, plants and certain
fungi A fungus (plural, : fungi or funguses) is any member of the group of Eukaryote, eukaryotic organisms that includes microorganisms such as yeasts and Mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified ...
. TPP riboswitches have also been predicted in archaea, but have not been experimentally tested.


History and discovery

Prior to the discovery of riboswitches, the mechanism by which some genes involved in multiple metabolic pathways were regulated remained mysterious. Accumulating evidence increasingly suggested the then-unprecedented idea that the mRNAs involved might bind metabolites directly, to affect their own regulation. These data included conserved RNA
secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...
s often found in the untranslated regions ( UTRs) of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers. In 2002, the first comprehensive proofs of multiple classes of riboswitches were published, including protein-free binding assays, and metabolite-binding riboswitches were established as a new mechanism of gene regulation. Many of the earliest riboswitches to be discovered corresponded to conserved sequence "motifs" (patterns) in 5' UTRs that appeared to correspond to a structured RNA. For example, comparative analysis of upstream regions of several genes expected to be co-regulated led to the description of the S-box (now the SAM-I riboswitch), the THI-box (a region within the TPP riboswitch), the RFN element (now the FMN riboswitch) and the B12-box (a part of the cobalamin riboswitch), and in some cases experimental demonstrations that they were involved in gene regulation via an unknown mechanism. Bioinformatics has played a role in more recent discoveries, with increasing automation of the basic comparative genomics strategy. Barrick ''et al.'' (2004) used BLAST to find UTRs
homologous Homology may refer to: Sciences Biology *Homology (biology), any characteristic of biological organisms that is derived from a common ancestor *Sequence homology, biological homology between DNA, RNA, or protein sequences * Homologous chrom ...
to all UTRs in '' Bacillus subtilis''. Some of these homologous sets were inspected for conserved structure, resulting in 10 RNA-like motifs. Three of these were later experimentally confirmed as the glmS, glycine and PreQ1-I riboswitches (see below). Subsequent comparative genomics efforts using additional taxa of bacteria and improved computer algorithms have identified further riboswitches that are experimentally confirmed, as well as conserved RNA structures that are hypothesized to function as riboswitches.


Mechanisms

Riboswitches are often conceptually divided into two parts: an aptamer and an expression platform. The aptamer directly binds the small molecule, and the expression platform undergoes structural changes in response to the changes in the aptamer. The expression platform is what regulates gene expression. Expression platforms typically turn off gene expression in response to the small molecule, but some turn it on. The following riboswitch mechanisms have been experimentally demonstrated. * Riboswitch-controlled formation of rho-independent transcription termination hairpins leads to premature transcription termination. * Riboswitch-mediated folding sequesters the
ribosome-binding site A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation. Mostly, RBS refers ...
, thereby inhibiting translation. * The riboswitch is a ribozyme that cleaves itself in the presence of sufficient concentrations of its metabolite. * Riboswitch alternate structures affect the splicing of the pre-mRNA. ** A TPP riboswitch in '' Neurospora crassa'' (a fungus) controls alternative splicing to conditionally produce an Upstream Open Reading Frame (uORF), thereby affecting the expression of downstream genes ** A TPP riboswitch in plants modifies splicing and alternative 3'-end processing * A riboswitch in '' Clostridium acetobutylicum'' regulates an adjacent gene that is not part of the same mRNA transcript. In this regulation, the riboswitch interferes with transcription of the gene. The mechanism is uncertain but may be caused by clashes between two RNA polymerase units as they simultaneously transcribe the same DNA. * A riboswitch in '' Listeria monocytogenes'' regulates the expression of its downstream gene. However, riboswitch transcripts subsequently modulate the expression of a gene located elsewhere in the genome. This ''trans'' regulation occurs via base-pairing to the mRNA of the distal gene. As the temperature of the bacterium increases, the riboswitch melts, allowing transcription. Unpublished undergraduate research created a similar riboswitch or 'thermosensor' via random mutagenesis of the Listeria monocytogenes sequence.


Types

The following is a list of experimentally validated riboswitches, organized by ligand. * ''
Cobalamin riboswitch Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' UTR, 5' untranslated regions of vitamin B12, vitamin B12 (Cobalamin) related genes in bacteria. Vitamin B12, Cobalamin (vitamin B12, coenzyme B12 ) riboswitches are ...
'' (also ''B12-element''), which binds either adenosylcobalamin (the coenzyme form of vitamin B12) or aquocobalamin to regulate cobalamin biosynthesis and transport of cobalamin and similar metabolites, and other genes. * ''
cyclic AMP-GMP riboswitch Cycle, cycles, or cyclic may refer to: Anthropology and social sciences * Cyclic history, a theory of history * Cyclical theory, a theory of American political history associated with Arthur Schlesinger, Sr. * Social cycle, various cycles in so ...
es'' bind the signaling molecule
cyclic AMP-GMP Cycle, cycles, or cyclic may refer to: Anthropology and social sciences * Cyclic history, a theory of history * Cyclical theory, a theory of American political history associated with Arthur Schlesinger, Sr. * Social cycle, various cycles in soc ...
. These riboswitches are structurally related to
cyclic di-GMP-I riboswitch Cyclic di-GMP-I riboswitches are a class of riboswitch that specifically bind cyclic di-GMP, which is a second messenger that is used in a variety of microbial processes including virulence, motility and biofilm formation. Cyclic di-GMP-I ...
es (see also "cyclic di-GMP" below). * '' cyclic di-AMP riboswitches'' (also called ''ydaO/yuaA'') bind the signaling molecule
cyclic di-AMP Cyclic di-AMP (also called c-di-AMP and c-di-adenosine monophosphate) is a second messenger used in signal transduction in bacteria and archaea. It is present in many Gram-positive bacteria, some Gram-negative species, and archaea of the phylum eu ...
. * ''cyclic di-GMP riboswitches'' bind the signaling molecule cyclic di-GMP in order to regulate a variety of genes controlled by this second messenger. Two classes of cyclic di-GMP riboswitches are known:
cyclic di-GMP-I riboswitch Cyclic di-GMP-I riboswitches are a class of riboswitch that specifically bind cyclic di-GMP, which is a second messenger that is used in a variety of microbial processes including virulence, motility and biofilm formation. Cyclic di-GMP-I ...
es and cyclic di-GMP-II riboswitches. These classes do not appear to be structurally related. * '' fluoride riboswitches'' sense fluoride ions, and function in surviving high levels of fluoride. * ''
FMN riboswitch The FMN riboswitch (also known as RFN element) is a highly conserved RNA element which is naturally occurring, and is found frequently in the 5'-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis ...
'' (also ''RFN-element'') binds flavin mononucleotide (FMN) to regulate
riboflavin Riboflavin, also known as vitamin B2, is a vitamin found in food and sold as a dietary supplement. It is essential to the formation of two major coenzymes, flavin mononucleotide and flavin adenine dinucleotide. These coenzymes are involved in ...
biosynthesis and transport. * '' glmS riboswitch'', which is a ribozyme that cleaves itself when there is a sufficient concentration of glucosamine-6-phosphate. * ''Glutamine riboswitches'' bind glutamine to regulate genes involved in glutamine and nitrogen metabolism, as well as short peptides of unknown function. Two classes of glutamine riboswitches are known: the '' glnA RNA motif'' and ''
Downstream-peptide motif The Downstream-peptide motif refers to a conserved RNA structure identified by bioinformatics in the cyanobacterial genera '' Synechococcus'' and '' Prochlorococcus'' and one phage that infects such bacteria. It was also detected in marine sampl ...
''. These classes are believed to be structurally related (see discussions in those articles). * ''
Glycine riboswitch The bacterial glycine riboswitch is an RNA element that can bind the amino acid glycine. Glycine riboswitches usually consist of two metabolite-binding aptamer domains with similar structures in tandem. The aptamers were originally thought to ...
'' binds glycine to regulate glycine metabolism genes, including the use of glycine as an energy source. Previous to 2012, this riboswitch was thought to be the only that exhibits cooperative binding, as it contains contiguous dual aptamers. Though no longer shown to be cooperative, the cause of dual aptamers still remains ambiguous. * ''
Lysine riboswitch The Lysine riboswitch is a metabolite binding RNA element found within certain messenger RNAs that serve as a precision sensor for the amino acid lysine. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results i ...
'' (also ''L-box'') binds
lysine Lysine (symbol Lys or K) is an α-amino acid that is a precursor to many proteins. It contains an α-amino group (which is in the protonated form under biological conditions), an α-carboxylic acid group (which is in the deprotonated −C ...
to regulate lysine biosynthesis, catabolism and transport. * '' manganese riboswitches'' bind manganese ions. * ''
NiCo riboswitch The NiCo riboswitch is a riboswitch that senses nickel or cobalt ions. Thus, it is an RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA ...
es'' bind the metal ions nickel and
cobalt Cobalt is a chemical element with the symbol Co and atomic number 27. As with nickel, cobalt is found in the Earth's crust only in a chemically combined form, save for small deposits found in alloys of natural meteoric iron. The free element, ...
. * ''PreQ1 riboswitches'' bind pre-queuosine1, to regulate genes involved in the synthesis or transport of this precursor to
queuosine Queuosine is a modified nucleoside that is present in certain tRNAs in bacteria and eukaryotes. It contains the nucleobase queuine. Originally identified in ''E. coli'', queuosine was found to occupy the first anticodon position of tRNAs for ...
. Three entirely distinct classes of PreQ1 riboswitches are known: PreQ1-I riboswitches,
PreQ1-II riboswitch PreQ1-II riboswitches form a class of riboswitches that specifically bind pre-queuosine1 (PreQ1), a precursor of the modified nucleoside queuosine. They are found in certain species of ''Streptococcus'' and ''Lactococcus'', and were originally i ...
es and
PreQ1-III riboswitch PreQ1-III riboswitches are a class of riboswitches that bind pre-queuosine1 (PreQ1), a precursor to the modified nucleoside queuosine. PreQ1-III riboswitches are the third class of riboswitches to be discovered that sense this ligand, and are struc ...
es. The binding domain of PreQ1-I riboswitches are unusually small among naturally occurring riboswitches. PreQ1-II riboswitches, which are only found in certain species in the genera ''Streptococcus'' and ''Lactococcus'', have a completely different structure, and are larger, as are PreQ1-III riboswitches. * ''
Purine riboswitch A purine riboswitch is a sequence of ribonucleotides in certain messenger RNA (mRNA) that selectively binds to purine ligands via a natural aptamer domain. This binding causes a conformational change in the mRNA that can affect translation by rev ...
es'' binds purines to regulate purine metabolism and transport. Different forms of the purine riboswitch bind guanine (a form originally known as the ''G-box'') or adenine. The specificity for either guanine or adenine depends completely upon Watson-Crick interactions with a single
pyrimidine Pyrimidine (; ) is an aromatic, heterocyclic, organic compound similar to pyridine (). One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has nitrogen atoms at positions 1 and 3 in the ring. The other ...
in the riboswitch at position Y74. In the guanine riboswitch this residue is always a cytosine (i.e. C74), in the adenine residue it is always a uracil (i.e. U74). Homologous types of purine riboswitches bind deoxyguanosine, but have more significant differences than a single nucleotide mutation. * ''
SAH riboswitch SAH riboswitches are a kind of riboswitch that bind S-adenosylhomocysteine (SAH). When the coenzyme S-adenosylmethionine (SAM) is used in a methylation reaction, SAH is produced. SAH riboswitches typically up-regulate genes involved in recycli ...
es'' bind S-adenosylhomocysteine to regulate genes involved in recycling this metabolite that is produced when
S-adenosylmethionine ''S''-Adenosyl methionine (SAM), also known under the commercial names of SAMe, SAM-e, or AdoMet, is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation. Although these anabolic reactions occur throug ...
is used in methylation reactions. * ''SAM riboswitches'' bind S-adenosyl methionine (SAM) to regulate
methionine Methionine (symbol Met or M) () is an essential amino acid in humans. As the precursor of other amino acids such as cysteine and taurine, versatile compounds such as SAM-e, and the important antioxidant glutathione, methionine plays a critical ro ...
and SAM biosynthesis and transport. Three distinct SAM riboswitches are known: '' SAM-I'' (originally called ''S-box''), '' SAM-II'' and the '' SMK box riboswitch''. SAM-I is widespread in bacteria, but SAM-II is found only in Alpha-, Beta-, and a few
Gammaproteobacteria Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genera-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically imp ...
. The SMK box riboswitch is found only in the order Lactobacillales. These three varieties of riboswitch have no obvious similarities in terms of sequence or structure. A fourth variety,
SAM-IV riboswitch SAM-IV riboswitches are a kind of riboswitch that specifically binds S-adenosylmethionine (SAM), a cofactor used in many methylation reactions. Originally identified by bioinformatics, SAM-IV riboswitches are largely confined to the Actinomyce ...
es, appears to have a similar ligand-binding core to that of SAM-I riboswitches, but in the context of a distinct scaffold. * '' SAM-SAH riboswitches'' bind both SAM and SAH with similar affinities. Since they are always found in a position to regulate genes encoding methionine adenosyltransferase, it was proposed that only their binding to SAM is physiologically relevant. * ''
Tetrahydrofolate riboswitch Tetrahydrofolate riboswitches are a class of homologous RNAs in certain bacteria that bind tetrahydrofolate (THF). It is almost exclusively located in the probable 5' untranslated regions of protein-coding genes, and most of these genes are kno ...
es'' bind tetrahydrofolate to regulate synthesis and transport genes. * '' TPP riboswitches'' (also THI-box) binds
thiamin pyrophosphate Thiamine pyrophosphate (TPP or ThPP), or thiamine diphosphate (ThDP), or cocarboxylase is a thiamine (vitamin B1) derivative which is produced by the enzyme thiamine diphosphokinase. Thiamine pyrophosphate is a cofactor that is present in all liv ...
(TPP) to regulate thiamin biosynthesis and transport, as well as transport of similar metabolites. It is the only riboswitch found so far in eukaryotes. * '' ZMP/ZTP riboswitches'' sense ZMP and ZTP, which are by-products of de novo purine metabolism when levels of 10-Formyltetrahydrofolate are low. Presumed riboswitches: * ''
Moco RNA motif The Moco RNA motif is a conserved RNA structure that is presumed to be a riboswitch that binds molybdenum cofactor or the related tungsten cofactor. Genetic experiments support the hypothesis that the Moco RNA motif corresponds to a genetic c ...
'' is presumed to bind molybdenum cofactor, to regulate genes involved in biosynthesis and transport of this coenzyme, as well as enzymes that use it or its derivatives as a cofactor. Candidate metabolite-binding riboswitches have been identified using bioinformatics, and have moderately complex
secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...
s and several highly conserved nucleotide positions, as these features are typical of riboswitches that must specifically bind a small molecule. Riboswitch candidates are also consistently located in the 5' UTRs of protein-coding genes, and these genes are suggestive of metabolite binding, as these are also features of most known riboswitches. Hypothesized riboswitch candidates highly consistent with the preceding criteria are as follows:
crcB RNA Motif The fluoride riboswitch (formerly called the ''crcB'' RNA motif) is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea. These RNAs were later shown to function as riboswitches that sense fluoride io ...
, manA RNA motif, pfl RNA motif, ydaO/yuaA leader,
yjdF RNA motif The ''yjdF'' RNA motif is a conserved RNA structure identified using bioinformatics. Most ''yjdF'' RNAs are located in bacteria classified within the phylum Bacillota. A ''yjdF'' RNA is found in the presumed 5' untranslated region (5' UTR) o ...
, ykkC-yxkD leader (and related ykkC-III RNA motif) and the
yybP-ykoY leader The yybP-ykoY leader RNA element was originally discovered in ''E. coli'' during a large scale screen and was named SraF. This family was later found to exist upstream of related families of protein genes in many bacteria, including the yybP and ...
. The functions of these hypothetical riboswitches remain unknown.


Computational models

Riboswitches have been also investigated using in-silico approaches. In particular, solutions for riboswitch prediction can be divided into two wide categories: * ''riboswitch gene finders'', i.e. systems aimed at uncovering riboswitches by genomic inspections, mostly based on motif-searching mechanisms. This group contains Infernal, the founding component of the Rfam database, and more specific tools such as RibEx or RiboSW. * ''conformational switch predictors'', i.e. methods based on a structural classification of alternative structures, such as paRNAss, RNAshapes and RNAbor. Moreover, family-specific approaches for ON/OFF structure prediction have been proposed as well. The SwiSpot tool somehow covers both the groups, as it uses conformational predictions to assess the presence of riboswitches.


The RNA world hypothesis

Riboswitches demonstrate that naturally occurring
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
can bind small molecules specifically, a capability that many previously believed was the domain of
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s or artificially constructed RNAs called aptamers. The existence of riboswitches in all domains of life therefore adds some support to the RNA world hypothesis, which holds that life originally existed using only RNA, and proteins came later; this hypothesis requires that all critical functions performed by proteins (including small molecule binding) could be performed by RNA. It has been suggested that some riboswitches might represent ancient regulatory systems, or even remnants of RNA-world ribozymes whose bindings domains are conserved.


As antibiotic targets

Riboswitches could be a target for novel antibiotics. Indeed, some antibiotics whose mechanism of action was unknown for decades have been shown to operate by targeting riboswitches. For example, when the antibiotic pyrithiamine enters the cell, it is metabolized into pyrithiamine pyrophosphate. Pyrithiamine pyrophosphate has been shown to bind and activate the TPP riboswitch, causing the cell to cease the synthesis and import of TPP. Because pyrithiamine pyrophosphate does not substitute for TPP as a coenzyme, the cell dies.


Engineered riboswitches

Since riboswitches are an effective method of controlling gene expression in natural organisms, there has been interest in engineering artificial riboswitches for industrial and medical applications such as gene therapy.


See also

*
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 ...
- Another class of mRNA regulatory segments which change conformation in response to temperature fluctuations, thereby exposing or occluding the ribosome binding site.


References


Further reading

* {{Authority control RNA Cis-regulatory RNA elements