Ribozyme applications

Riboswitches

Riboswitches are structured noncoding RNA domains which are typically embedded in messenger RNAs in many bacteria, where they monitor the concentrations of their target ligands and regulate gene expression accordingly. Typically, riboswitches are composed of two parts: an aptamer that senses the target ligand and an expression platform that directly interfaces with components of the cell that affect gene expression. In the past 20 years, more than 55 riboswitch classes have been experimentally validated and the ligands they sense comprise a diverse list of biologically relevant compounds including fundamental metabolites derived from RNA nucleotides or their precursors, amino acid, elemental ions and et al. The database also incorporates the T-box to exemplify the sophisticated mechanisms of tRNA recognition in Gram-positive bacteria. Nevertheless, it is important to note that the database does not encompass all conceivable categories, including notable examples like RNA thermometers, pH-responsive elements, ATP-sensing leader mRNAs, and others. For more detailed information about each riboswitch, please browse the table below and click on each riboswitch name.

Statistical information

Classification of experimentally validated riboswitches. The plotted data correspond to the types of riboswitches according to the biochemical category of their cognate ligand.This panel was adapted from Ron Breaker (Salvail,H. and Breaker,R.R. Curr. Biol. 2023)

Detail information

This section lists all the experimentally validated riboswitches.

Cofactors

Name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
AdoCbl	Adenosylcobalamin	Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' untranslated regions of cobalamin related genes in bacteria to regulate adjacent genes related to cobalamin metabolism in response to cobalamin binding. Cobalamin riboswitches are broadly classified by the identity of the aptamer, and can be further classified into AdoCbl and AqCbl riboswitch.	2000	AdoCbl riboswitch Cobalamin riboswitch	RF01482 RF00174
AqCbl	Aquocobalamin	Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' untranslated regions of cobalamin related genes in bacteria to regulate adjacent genes related to cobalamin metabolism in response to cobalamin binding. Cobalamin riboswitches are broadly classified by the identity of the aptamer, and can be further classified into AdoCbl and AqCbl riboswitch.	2000	AdoCbl variant RNA	RF01689
FMN	Flain mononucleotide	The FMN riboswitch (also known as RFN element) is a highly conserved RNA element which is found frequently in the 5'-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. This element is a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins, thus giving it the ability to regulate RNA expression by responding to changes in the concentration of FMN.	1999	FMN riboswitch (RFN element)	RF00050
MoCo	Molybdenum cofactor	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. As these cofactors are not available in purified form, in vitro binding assays cannot be performed. However, the genetic data, complex structure of the RNA and the failure to detect a protein involved in the regulation suggest that the Moco RNA motif corresponds to a class of riboswitches.	2007	Moco (molybdenum cofactor) riboswitch	RF01055
Wco	Tungsten cofactor	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. As these cofactors are not available in purified form, in vitro binding assays cannot be performed. However, the genetic data, complex structure of the RNA and the failure to detect a protein involved in the regulation suggest that the Moco RNA motif corresponds to a class of riboswitches.	2007	None	None
THF-I	Tetrahydrofolate	THF riboswitches are a class of homologous RNAs in certain bacteria that bind tetrahydrofolate (THF) which are almost exclusively located in the probable 5' UTR of protein-coding genes, encoding either folate transporters or enzymes involved in folate metabolism. THF riboswitches are found in a variety of Bacillota, specifically the orders Clostridiales and Lactobacillales, and more rarely in other lineages of bacteria.	2010	THF riboswitch	RF01831
THF-II	Tetrahydrofolate	THF-II riboswitch (also known as folE RNA motif) is a conserved RNA structure that was discovered by bioinformatics. All known folE RNAs are present upstream of genes encoding GTP cyclohydrolase I, which performs a step in folate metabolism. folE RNAs have been shown to bind tetrahydrofolate and related molecules, leading to their designation as a second structural class of tetrahydrofolate riboswitches, called THF-II riboswitches.	2017	folE RNA	RF02977
TPP	Thiamin pyrophosphate	The TPP riboswitch, also known as the THI element and Thi-box riboswitch, is a highly conserved RNA secondary structure. It binds thiamine pyrophosphate (TPP) directly and modulates gene expression through a variety of mechanisms in archaea, bacteria and eukaryotes.	2001	TPP riboswitch (THI element)	RF00059
HMP-PP	Hydroxymethyl-pyrimidine pyrophosphate	HMP-PP riboswitches are a class of homologous RNAs in certain bacteria that function as sensors of the thiamin precursor HMP-PP. The HMP-PP riboswitch was initially named as the ‘thiS motif’ because of its frequent association with a gene coding for the ThiS protein, which delivers sulfur to form the thiazole moiety of the thiamin precursor HET-P. The 3D structure of the HMP-PP riboswitch has not been solved yet.	2019	None	None
SAM-I	S-adenosylmethionine	This family is a member of clan (CL00012), which contains the following 3 members:SAM-I, SAM-I-IV-variant, SAM-IV, they are a kind of riboswitch that specifically binds S-adenosylmethionine (SAM), whose members share a common binding core but have widely divergent peripheral architectures.	1998	SAM riboswitch (S box leader)	RF00162
SAM-IV	S-adenosylmethionine	This family is a member of clan (CL00012), which contains the following 3 members:SAM-I, SAM-I-IV-variant, SAM-IV, they are a kind of riboswitch that specifically binds S-adenosylmethionine (SAM), whose members share a common binding core but have widely divergent peripheral architectures.	2007	S-adenosyl methionine (SAM) riboswitch	RF00634
SAM-I/IV	S-adenosylmethionine	This family is a member of clan (CL00012), which contains the following 3 members:SAM-I, SAM-I-IV-variant, SAM-IV, they are a kind of riboswitch that specifically binds S-adenosylmethionine (SAM), whose members share a common binding core but have widely divergent peripheral architectures.	2010	SAM-I/IV variant riboswitch	RF01725
SAM-II	S-adenosylmethionine	This family consists of two members: SAM-II and SAM-V riboswitch, The SAM-II riboswitch is a RNA element found predominantly in Alphaproteobacteria that binds S-adenosyl methionine (SAM). SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine (SAM).	2005	SAM riboswitch (alpha-proteobacteria)	RF00521
SAM-V	S-adenosylmethionine	This family consists of two members: SAM-II and SAM-V riboswitch, The SAM-II riboswitch is a RNA element found predominantly in Alphaproteobacteria that binds S-adenosyl methionine (SAM). SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine (SAM).	2009	SAM-V riboswitch	RF01826
SAM-III	S-adenosylmethionine	The S_MKbox riboswitch (also known as SAM-III) is an RNA element that regulates gene expression in bacteria.	2006	SMK box translational riboswitch (SAM-III)	RF01767
SAM-VI	S-adenosylmethionine	SAM-VI is predominantly found in Bifidobacterium and exhibits some similarities to the SAM-III (Smk box) riboswitch class	2018	SAM-VI riboswitch	RF02885
SAM-SAH	S-adenosylmethionine and S-adenosylhomocysteine	The SAM–SAH riboswitch is a conserved RNA structure in certain bacteria that binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) and is therefore presumed to be a riboswitch.	2010	SAM/SAH riboswitch	RF01727
SAH	S-adenosylhomocysteine	SAH riboswitches are a kind of riboswitch that bind S-adenosylhomocysteine (SAH). SAH riboswitches typically up-regulate genes involved in recycling SAH to create more SAM (or the metabolically related methionine).	2008	S-adenosyl-L-homocysteine riboswitch	RF01057
NAD⁺-I	Nicotinamide adenine dinucleotide	NAD⁺-I riboswitch is the first class of riboswitches that recognize NAD⁺. It is usually located upstream of nadA genes within the phylum Acidobacteria, which encode quinolinate synthetase, an enzyme that performs a step in NAD⁺ synthesis.	2017	nadA RNA	RF03013
NAD⁺-II	Nicotinamide adenine dinucleotide	NAD⁺-II riboswitch is the second class of riboswitches that recognize NAD⁺. It is usually associated with pnuC genes, and PnuC proteins are known to transport nicotinamide riboside (NR), which is a component of the ubiquitous and abundant enzyme cofactor nicotinamide adenine dinucleotide (NAD⁺).	2021	None	None

RNA derivatives

Name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
Xanthine-I	Xanthine	There are two classes of xanthine riboswitches. The xanthine-I riboswitch, formerly known as the NMT1 motif RNA, is tightly binds 8-azaxanthine, xanthine, and uric acid. Xanthine-II riboswitch is a class of xanthine-sensing guanine riboswitch variants.	2020	Xanthine riboswitch (NMT1 RNA)	RF03054
Xanthine-II	Xanthine	There are two classes of xanthine riboswitches. The xanthine-I riboswitch, formerly known as the NMT1 motif RNA, is tightly binds 8-azaxanthine, xanthine, and uric acid. Xanthine-II riboswitch is a class of xanthine-sensing guanine riboswitch variants.	2022	None	NA
2'-dG-I	2'-Deoxyguanosine	Carrying an aptamer domain similar in sequence and secondary structure to the guanine riboswitch, the 2'-dG-I riboswitch exhibits improved affinities for 2'-deoxyguanosine (2'-dG) and guanosine, and contains a uracil ribonucleotide in a conserved position of the ligand-binding aptamer domain. The 2'-dG-I riboswitch has atomic-resolution structural model.	2007	Purine riboswitch	RF00167
2'-dG-II	2'-Deoxyguanosine	Carrying an aptamer domain similar in sequence and secondary structure to the guanine riboswitch, the 2'-dG-II riboswitch exhibits improved affinities for 2'-deoxyguanosine (2'-dG), 3'-deoxyguanosine (3'-dG) and guanosine, and contains a uracil ribonucleotide in a conserved position of the ligand-binding aptamer domain. The 2'-dG-II riboswitch also has atomic-resolution structural model.	2017	2dG-II	RF03165
2'-dG-III	2'-Deoxyguanosine	Carrying an aptamer domain similar in sequence and secondary structure to the guanine riboswitch, the 2'-dG-III riboswitch exhibits improved affinities for 2'-deoxyguanosine (2'-dG), 3'-deoxyguanosine (3'-dG) and guanosine, and contains a uracil ribonucleotide in a conserved position of the ligand-binding aptamer domain	2022	None	None
PreQ₁-I	Prequeusine-1	PreQ₁ is a guanine-derived nucleobase that is known to be incorporated in the wobble position of tRNAs containing the GUN anticodon sequence and then further modified to yield queuosine (Q). PreQ₁-I has a distinctly small aptamer, ranging from 25 to 45 nucleotides long, and it is represented by RNAs sub-classified as 'type 1', 'type 2' and 'type 3'.	2007	PreQ1 riboswitch	RF00522
PreQ₁-II	Prequeusine-1	PreQ₁-II riboswitch, only found in Lactobacillales, has a larger and more complex consensus sequence and structure than preQ₁-I riboswitch, with an average of 58 nucleotides composing its aptamer, which forms as many as five base-paired substructures	2008	preQ1-II (pre queuosine) riboswitch	RF01054
preQ₁-III	Prequeusine-1	PreQ₁-III riboswitch has a distinct structure and is also larger in aptamer size than preQ₁-I riboswitch, ranging from 33 to 58 nucleotides.	2014	PreQ1-III riboswitch	RF02680

RNA precursors

name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
Adenine	Adenine	Carrying an aptamer domain similar in sequence and secondary structure to the guanine riboswitch, the adenine riboswitch selectively recognizes adenine, and contains a uracil ribonucleotide in position 74 of the adenine-binding aptamer domain. B. subtilis ydhL (also called pbuE) and two RNAs (add genes) from Clostridium perfringens and Vibrio vulnificus harbor adenine riboswitches in their mRNA elements.	2004	Purine riboswitch	RF00167
Guanine-I	Guanine	The guanine riboswitch selectively recognizes guanine, and contains a cytosine ribonucleotide in a specific position of the guanine-binding aptamer domain, most commonly associated with genes encoding phosphoribosyltransferase (PRT) enzymes. The guanine-I riboswitch has been shown to control gene expression through transcriptional termination.	2003	Purine riboswitch	RF00167
Guanine-II	Guanine	The guanine riboswitch selectively recognizes guanine, and contains a cytosine ribonucleotide in a specific position of the guanine-binding aptamer domain, most commonly associated with genes encoding phosphoribosyltransferase (PRT) enzymes. The guanine-II riboswitch is consistent with a genetic "ON" switch.	2022	Purine riboswitch	RF00167
PRPP	Phosphoribosyl Pyrophosphate	The ykkC RNAs were initially found in 2004. Phosphoribosyl pyrophosphate (PRPP, 5-phospho-α-D-ribose 1-diphosphate) was identified as the ligand for ykkC subtype 2b RNAs (PRPP riboswitches).	2018	None	None
PRA	5-phospho-Dribosylamine	The PRA riboswitch (Fibro-purF RNA motif) is a conserved RNA structure that was discovered by bioinformatics. All known Fibro-purF RNAs are found upstream of purF genes, which encode amidophosphoribosyltransferase that participates in the biosynthesis of biological purine molecules.	2020	Fibro-purF RNA	RF02974
ADP	Adenosine diphosphate	The ykkC RNAs were initially found in 2004. The ykkC subtype 2c RNAs were proved to recognize adenosine and cytidine 5′-diphosphate molecules in either their ribose or deoxyribose forms (ADP, dADP, CDP, and dCDP) in 2019.	2019	None	None

Signaling molecules

Name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
c-AMP-GMP	Cyclic AMP-GMP	The c-AMP-GMP riboswitch (also known as c-GAMP riboswitch) form a class of riboswitch that binds specifically to cyclic AMP-GMP. Previously annotated as the c-di-GMP-I riboswitch, its mutant c-AMP-GMP riboswitch is able to bind to a second messenger, c-AMP-GMP. The c-AMP-GMP riboswitch recognizes c-AMP-GMP and controls a group of genes important for utilizing iron oxide (III) in external power generation. The riboswitch are predominantly found in species of Bacillales, Clostridia, Deltaproteobacteria, and Gammaproteobacteria .	2015	None	None
ppGpp	Guanosine tetraphosphate	The ppGpp riboswitches, originally identified by bioinformatics and classified as subtypes 2a of "The ykkC motif", form a class of riboswitch that specifically bind guanosine tetraphosphate (ppGpp), which is a well-known alarmone produced during various stresses including stringent response, causing by a shortage of amino acids. The ppGpp riboswitches control genes involved in biosynthesis and transport of branched-chain amino acids and genes encoding for glutamate synthase and the ATP-binding cassette transporters (ABC transporters).	2018	None	None
c-di-GMP	Cyclic di-GMP	The c-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. The c-di-GMP-I riboswitches were originally identified by bioinformatics as a conserved RNA-like structure called the "GEMM motif". These riboswitches are present in a wide variety of bacteria, and are most common in Clostridia and certain varieties of Pseudomonadota. The riboswitches are present in pathogens such as Clostridium difficile, Vibrio cholerae (which causes cholera) and Bacillus anthracis (which causes anthrax). Geobacter uraniumreducens is predicted to have 30 instances of this riboswitch in its genome. A bacteriophage that infects C. difficile is predicted to carry a cyclic di-GMP-I riboswitch, which it might use to detect and exploit the physiological state of bacteria that it infects.	2008	Cyclic di-GMP-I riboswitch c-di-GMP-I-GGC riboswitch c-di-GMP-I-UAU riboswitch	RF01051 RF03167 RF03168
c-di-GMP-II	Cyclic di-GMP	The c-di-GMP-II riboswitches form a class of riboswitches that specifically bind cyclic di-GMP, a second messenger used in multiple bacterial processes such as virulence, motility and biofilm formation. The c-di-GMP-II riboswitches are structurally unrelated to c-di-GMP-I riboswitches, though they have the same function. The c-di-GMP-II riboswitches were discovered by bioinformatics, and are common in species within the class Clostridia and the genus Deinococcus. They are also found in some other bacterial lineages. There is significant overlap between species that use c-di-GMP-I and c-di-GMP-II riboswitches, as both riboswitch classes are common in Clostridia.	2010	Cyclic di-GMP-II riboswitch c-di-GMP-II-GAG riboswitch c-di-GMP-II-GCG riboswitch	RF01786 RF03169 RF03170
c-di-AMP	Cyclic di-AMP	The YdaO/YuaA leader (now called the c-di-AMP riboswitch) is a conserved RNA structure found upstream of the ydaO and yuaA genes in Bacillus subtilis and related genes in other bacteria. Its secondary structure and gene associations were predicted by bioinformatics. These RNAs function as riboswitches, and sense the signaling molecule cyclic di-AMP.	2013	YdaO/YuaA leader	RF00379
ZTP	ZTP	The ZMP/ZTP riboswitch (called the pfl RNA motif before) refers to a conserved RNA structure present in some bacteria and originally discovered using bioinformatics. ZMP/ZTP riboswitch is consistently present in genomic locations that likely correspond to the 5' UTRs of protein-coding genes. This arrangement in bacteria is commonly associated with cis-regulatory elements.	2015	ZMP/ZTP riboswitch	RF01750

Elemental ions

name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
Fluoride	F^-	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 ions. These "fluoride riboswitches" increase expression of downstream genes when fluoride levels are elevated, and the genes are proposed to help mitigate the toxic effects of very high levels of fluoride.	2010	Fluoride riboswitch (crcB)	RF01734
Mg²⁺-I	Mg²⁺-I	The Ykok leader or M-box is a Mg-sensing RNA structure that controls the expression of Magnesium ion transport proteins in bacteria. It is a distinct structure to the Magnesium responsive RNA element. Examples of the conserved M-box RNA structure occur upstream of each of the three major families of Mg transporters (CorA, MgtE and MgtA/MgtB) in various bacterial species.	2004	M-box riboswitch (ykoK leader)	RF00380
Mg²⁺-II	Mg²⁺-I	The Magnesium responsive RNA element is a cis-regulatory element that regulates the expression of the magnesium transporter protein MgtA. It is located in the 5' UTR of this gene. A recent report suggests that the RNA element targets the mgtA transcript for degradation by RNase E when cells are grown in high Mg²⁺ environments.	2006	Magnesium Sensor	RF01056
Mn²⁺	Mn²⁺	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 the yybP and ykoY genes in B. subtilis. TheyybP-ykoY element was later proposed to be manganese-responsive after another associated family of genes, YebN/MntP, was shown to encode Mn efflux pumps in several bacteria. Genetic data and a crystal structure confirmed that yybP-ykoY is a manganese riboswitch that directly binds Mn²⁺.	2004	yybP-ykoY manganese riboswitch	RF00080
NiCo	Ni²⁺ and Co²⁺	The NiCo riboswitch is a riboswitch that senses nickel or cobalt ions. Iron responsiveness is also a generalproperty of the czcD family. Thus, it is an RNA molecule that specifically binds these metal ions, and regulates genes accordingly.	2015	NiCo riboswitch	RF02683
Na⁺-I	Na⁺-I	The DUF1646 RNA motif is a conserved RNA structure that was discovered by bioinformatics. The genes apparently regulated by DUF1646 RNAs are often related to the transportation of sodium ions. A DUF1646 RNA occurs upstream of an operon in Enterococcus hirae that was shown to regulate the downstream genes based on sodium ion concentrations. However, it is unclear whether this DUF1646 RNA participates in sodium-based gene regulation.	2017	Na+ riboswitch (DUF1646 RNA)	RF03071
Na⁺-II	Na⁺-I	None	None	None	None
Li⁺-I	Li⁺	The nhaA-I RNA motif is a conserved RNA structure that was discovered by bioinformatics. nhaA-I motif RNAs are found in Acidobacteriota, alpha-, beta- and Gammaproteobacteria, Verrucomicrobiota and the tentative phylum NC10. nhaA-I RNAs typically occur upstream of genes that encode exchangers of sodium ions and protons. In 2022, Breaker et al. identified nhaA-I motif as Li⁺-I riboswitches.	2017	nhaA-I RNA	RF03057
Li⁺-II	Li⁺	The nhaA-II RNA motif is a conserved RNA structure that was discovered by bioinformatics. nhaA-II motifs are found in Caulobacterales.nhaA-I RNAs typically occur upstream of genes that encode exchangers of sodium ions and protons. In 2022, Breaker et al. identified nhaA-II motif as Li⁺-II riboswitches.	2017	nhaA-II RNA	RF03038

Amino acids

Name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
Glycine	Glycine	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 cooperatively bind glycine to regulate the expression of downstream genes. It is thought that when glycine is in excess it will bind to both aptamers to activate these genes and facilitate glycine degradation.	2004	Glycine riboswitch	RF00504
Lysine	Lysine	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 in modulation of gene expression. Lysine riboswitch are most abundant in Bacillota and Gammaproteobacteria where they are found upstream of a number of genes involved in lysine biosynthesis, transport and catabolism.	2003	Lysine riboswitch	RF00168
Glutamine-I	Glutamine	The glutamine riboswitch is a conserved RNA structure that can bind glutamine. It is present in a variety of lineages of cyanobacteria, as well as some phages that infect cyanobacteria. It is also found in DNA extracted from uncultivated bacteria living in the ocean that are presumably species of cyanobacteria. glnA RNAs are found in the presumed 5' untranslated regions of genes encoding multiple classes of protein that are involved in nitrogen metabolism. The most prominent of these protein classes are ammonium transporters, the enzymes glutamine synthetase and glutamate synthase and PII protein, which itself regulates nitrogen metabolism.	2011	Glutamine riboswitch	RF01739
Glutamine-II	Glutamine	The glutamine-II riboswitch is a conserved RNA structure that can bind glutamine. It 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 samples of DNA from uncultivated bacteria, which are presumably other species of cyanobacteria.	2011	Glutamine-II riboswitch (downstream peptide RNA)	RF01704

Sugars

name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
GlcN6P	Glucosamine-6-phosphate	The glucosamine-6-phosphate riboswitch (GlcN6P riboswitch) is an RNA structure that regulates the glmS gene by responding to concentrations of GlcN6P, while also catalyzing a self-cleaving chemical reaction. This leads to the degradation of the mRNA containing the ribozyme, lowering production of GlcN6P. GlcN6P is essential for cell wall biosynthesis and the glmS gene encodes for an enzyme that catalyzes its formation from fructose-6-phosphate and glutamine. The RNA is the first riboswitch found to be a self-cleaving ribozyme, discovered through bioinformatics.	2004	glmS glucosamine-6-phosphate activated ribozyme	RF00234

T-box

Name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
T-box	tRNA	Usually found in gram-positive bacteria, the T box leader sequence is an RNA element that controls gene expression through the regulation of translation by binding directly to a specific tRNA and sensing its aminoacylation state. This interaction controls expression of downstream aminoacyl-tRNA synthetase genes, amino acid biosynthesis, and uptake-related genes in a negative feedback loop. The uncharged tRNA acts as the effector for transcription antitermination of genes in the T-box leader family. The anticodon of a specific tRNA base pairs to a specifier sequence within the T-box motif, and the NCCA acceptor tail of the tRNA base pairs to a conserved bulge in the T-box antiterminator hairpin.	1992	T-box leader	RF00230

Others

Name	Ligand	Description	Discovery	Rfam-name	Rfam-ID
Azaaromatic	Azaaromatic	The azaaromatic riboswitch was named yjdF RNA. yjdF RNAs appear to function as riboswitches that sense azaaromatic compounds, although the precise compound or set of compounds that is sensed by this riboswitch in the cell remains unclear. Most yjdF RNAs are located in bacteria classified within the phylum Bacillota.	2016	yjdF RNA	RF01764
Guanidine-I	Guanidine	Four classes of riboswitches have been identified that bind the cationic molecule guanidine (Gdm⁺ ). Now known as guanidine-I, -II, -III and -IV riboswitches.	2017	Guanidine-I riboswitch	RF00442
Guanidine-II	Guanidine	Four classes of riboswitches have been identified that bind the cationic molecule guanidine (Gdm⁺ ). Now known as guanidine-I, -II, -III and -IV riboswitches.	2017	Guanidine-II riboswitch	RF01068
Guanidine-III	Guanidine	Four classes of riboswitches have been identified that bind the cationic molecule guanidine (Gdm⁺ ). Now known as guanidine-I, -II, -III and -IV riboswitches.	2017	Guanidine-III riboswitch	RF01763
Guanidine-IV	Guanidine	Four classes of riboswitches have been identified that bind the cationic molecule guanidine (Gdm⁺ ). Now known as guanidine-I, -II, -III and -IV riboswitches.	2020	None	None