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Part of a messenger RNA molecule
In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production
Riboswitch
Chemical compound found in all domains of life with largely unexplored effects
methyltransferase SAM-I riboswitch SAM-II riboswitch SAM-III riboswitch SAM-IV riboswitch SAM-V riboswitch SAM-VI riboswitch List of investigational antidepressants
S-Adenosyl_methionine
RNA family
A purine riboswitch is a sequence of ribonucleotides in certain messenger RNA (mRNA) that selectively binds to purine ligands via a natural aptamer domain
Purine_riboswitch
Chemical compound and essential nutrient
the biosynthesis are produced. The specific riboswitch, the TPP riboswitch, is the only known riboswitch found in both eukaryotic and prokaryotic organisms
Thiamine
RNA family
queuosine pathway, and preQ1 riboswitch, as a type of riboswitch, is an RNA element that binds preQ1. The preQ1 riboswitch is distinguished by its unusually
PreQ1_riboswitch
RNA family
Riboswitch_s0670 is a probable SAM riboswitch identified by RNA deep sequencing of Clostridioides difficile 630. Close matches are found with members
Riboswitch_s0670
RNA family
SAH riboswitches are a kind of riboswitch that bind S-adenosylhomocysteine (SAH). When the coenzyme S-adenosylmethionine (SAM) is used in a methylation
SAH_riboswitch
upstream of queT genes. The atomic-resolution structure of a preQ1-III riboswitch has been solved by X-ray crystallography. McCown PJ, Liang JJ, Weinberg
PreQ1-III_riboswitch
Class of homologous RNAs
Lactobacillales, and more rarely in other lineages of bacteria. The THF riboswitch was one of many conserved RNA structures found in a project based on comparative
Tetrahydrofolate_riboswitch
RNA family
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
Lysine_riboswitch
Glutamine-binding RNA structure
The glutamine riboswitch (formerly glnA RNA motif) is a conserved RNA structure that was predicted by bioinformatics. It is present in a variety of lineages
Glutamine_riboswitch
Fluoride-binding RNA structure
The fluoride riboswitch (formerly called the crcB RNA motif) is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and
Fluoride_riboswitch
American geneticist (1925–2018)
establishment of the one gene-one enzyme hypothesis and discovered attenuation, a riboswitch mechanism in which messenger RNA changes shape in response to a small
Charles_Yanofsky
Highly conserved RNA element
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
FMN_riboswitch
RNA family
The NAD⁺-II riboswitch (also called the pnuC RNA motif) is a riboswitch found in bacteria that regulates gene expression in response to levels of nicotinamide
NAD-II_riboswitch
RNA family
Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' untranslated regions of vitamin B12 (Cobalamin) related genes in bacteria
Cobalamin_riboswitch
Conserved RNA structure
The NAD-I riboswitch (also known as the nadA RNA motif) is a conserved RNA structure found in bacteria, primarily within the phylum Acidobacteriota. All
NAD-I_riboswitch
RNA family
The NiCo riboswitch is a riboswitch that senses nickel or cobalt ions. Thus, it is an RNA molecule that specifically binds these metal ions, and regulates
NiCo_riboswitch
RNA secondary structure
The TPP riboswitch, also known as the THI element and Thi-box riboswitch, is a highly conserved RNA secondary structure. It serves as a riboswitch that binds
TPP_riboswitch
RNA element
The bacterial glycine riboswitch is an RNA element that can bind the amino acid glycine. Glycine riboswitches usually consist of two metabolite-binding
Glycine_riboswitch
RNA family
SAH riboswitch SAM-I riboswitch SAM-II riboswitch SAM-IV riboswitch SAM-V riboswitch SAM-VI riboswitch SAM-Chlorobi RNA motif SAM–SAH riboswitch Lu C
SMK_box_riboswitch
RNA family
SAM-IV riboswitches are a kind of riboswitch that specifically binds S-adenosylmethionine (SAM), a cofactor used in many methylation reactions. Originally
SAM-IV_riboswitch
RNA family
riboswitches, as both riboswitch classes are common in Clostridia. In Clostridioides difficile (bacteria) strains, a cyclic di-GMP-II riboswitch is found adjacent
Cyclic_di-GMP-II_riboswitch
RNA family
The SAM riboswitch (also known as the S-box leader and the SAM-I riboswitch) is found upstream of a number of genes which code for proteins involved in
SAM_riboswitch_(S-box_leader)
analysis of Bifido-meK motif RNAs. SAM-I riboswitch SAM-II riboswitch SAM-III riboswitch SAM-IV riboswitch SAM-V riboswitch Gayan, Mirihana Arachchilage; Sherlock
SAM-VI_riboswitch
Bacterial RNA structure
The SAM–SAH riboswitch is a conserved RNA structure in certain bacteria that binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) and is therefore
SAM–SAH_riboswitch
Bacterial enzyme
for containing a riboswitch, a structure in its messenger RNA that prevents its translation when bound to lysine. Such lysine riboswitch thus acts as a
LysC
Class of riboswitches
secondary structure called the "COG4708 motif". All known members of this riboswitch class appear to control members of COG4708 genes. These genes are predicted
PreQ1-II_riboswitch
RNA family
SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine (SAM). It was first discovered in the marine bacterium Candidatus Pelagibacter
SAM-V_riboswitch
RNA family
Mutagenesis confirmed that changing nucleotides within the loop regions of this riboswitch altered the specificity for ligand binding. This study showed that the
Mesoplasma_florum_riboswitch
RNA family
single hairpin and a pseudoknot. SAM-I riboswitch SAM-III riboswitch SAM-IV riboswitch SAM-V riboswitch SAM-VI riboswitch Corbino KA, Barrick JE, Lim J, et al
SAM-II_riboswitch
RNA family
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
Cyclic_di-GMP-I_riboswitch
Species of bacterium
metagenomic data. Examples of ncRNA found in these organisms include the SAM-V riboswitch, and other cis-regulatory elements like the rpsB motif. Another example
Pelagibacter_communis
RNA family
The pfl RNA motif (now called the ZMP/ZTP riboswitch) refers to a conserved RNA structure present in some bacteria and originally discovered using bioinformatics
Pfl_RNA_motif
Conserved RNA structure in bacteria
Nelson et al. showed that this riboswitch senses and responds to guanidine and it was renamed Guanidine-I riboswitch. Furthermore, they demonstrated
YkkC-yxkD_leader
RNA element
mismatched, the T box riboswitch and tRNA complex is disrupted, and proper functioning of transcriptional regulation cannot occur. The riboswitch functions by
T-box_leader
RNA element
structured RNA element may be involved in their genetic regulation as a riboswitch. The yybP-ykoY element was later proposed to be manganese-responsive after
YybP-ykoY_leader
RNA family
lmo0518 5′-UTR-derived Putative riboswitch. rli53 955829 956001 172 lmo0918 -> -> -> lmo0919 5′-UTR-derived Putative riboswitch. rli54 1078584 1079111 527
Listeria monocytogenes non-coding RNA
Listeria_monocytogenes_non-coding_RNA
Chemical compound
chemical compound which is found to be a potent inhibitor of the FMN riboswitch, meaning it could serve as a promising lead compound for developing a
Ribocil
RNA structure in bacteria
The YdaO/YuaA leader (now called the cyclic di-AMP riboswitch) is a conserved RNA structure found upstream of the ydaO and yuaA genes in Bacillus subtilis
YdaO/yuaA_leader
Malaysian biologist
Fellowship and the Yale College Dean’s Research Fellowship for his work on riboswitch biochemistry and RNA splicing under the mentorship of Dr. Ronald Breaker
Ming_Tatt_Cheah
Topics referred to by the same term
to: Rainforest Foundation Norway Rifleman Russian Federation Navy FMN riboswitch (also known as RFN element) This disambiguation page lists articles associated
RFN
Disputed genetic element
antibiotic-resistant genes and that functions as an aminoglycoside-specific riboswitch. The putative RNA is upstream of aminoglycoside acetyl transferase (AAC)
AAC/AAD_leader
RNA family
the glnA RNA motif which was shown to be a functional glutamine binding riboswitch in cyanobacteria. The most striking similarity is the nucleotide conservation
Downstream-peptide_motif
Order of bacteria
Breaker & Stephen J. Giovannoni (January 2009). "Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11". Environmental Microbiology
Pelagibacterales
Chemical compound
begins with GTP. In bacteria, three structurally unrelated classes of riboswitch are known to regulate genes that are involved in the synthesis or transport
Queuosine
It can be used to look for nucleic acid and protein motifs, including riboswitch-like elements, upstream open reading frames (uORFs), short open reading
DIMPL
RNA family
sequence conservation of DUF1646 RNA Identifiers Symbol DUF1646 Rfam RF03071 Other data RNA type Cis-reg; Riboswitch SO SO:0000035 PDB structures PDBe
DUF1646_RNA_motif
Species of bacterium
S2CID 20882401. Jorth P, Whiteley M (December 2010). "Characterization of a novel riboswitch-regulated lysine transporter in Aggregatibacter actinomycetemcomitans"
Aggregatibacter actinomycetemcomitans
Aggregatibacter_actinomycetemcomitans
Nucleic acid sequence
simplified example of the flavin mononucleotide (FMN) riboswitch is shown in the illustration. This riboswitch exists in the mRNA transcript and has several stem-loop
Inverted_repeat
Chemical compound
ylid: A full view of TPP. The arrow indicates the acidic proton. TPP riboswitch Pietrzak I (1995). "[Vitamin disturbances in chronic renal insufficiency
Thiamine_pyrophosphate
RNA family
are also very commonly regulated by the previously established ZMP/ZTP riboswitch. These ZMP/ZTP-sensing riboswitches detect a shortage of formyltetrahydrofolate
FTHFS_RNA_motif
Explanation of the flow of genetic information within a biological system
Gene expression Epigenetics Genome Alternative splicing Genetic code Riboswitch Leavitt SA (June 2010). "Deciphering the Genetic Code: Marshall Nirenberg"
Central dogma of molecular biology
Central_dogma_of_molecular_biology
Adjustment within a biological system
Shine-Dalgarno sequence) located on the same transcript as the Riboswitch. The Riboswitch stem-loop has a region complementary to the Shine-Dalgarno but
Autoregulation
Biochemist (born 1961)
Azoarcus Group I catalytic intron, the glmS ribozyme, and the c-di-GMP riboswitch. He has also collaborated with the Thomas A. Steitz lab at Yale on structural
Scott_Strobel
RNA family
The folE RNA motif, now known as the THF-II riboswitch, is a conserved RNA structure that was discovered by bioinformatics. folE motifs are found in Alphaproteobacteria
FolE_RNA_motif
Class of enzymes
the GS inactivating factor IF17 is controlled by a glutamine-binding riboswitch. PDB: 1FPY; Gill HS, Eisenberg D (February 2001). "The crystal structure
Glutamine_synthetase
RNA family
responsive RNA element, not to be confused with the completely distinct M-box riboswitch, is a cis-regulatory element that regulates the expression of the magnesium
Magnesium responsive RNA element
Magnesium_responsive_RNA_element
RNA family
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
Moco_RNA_motif
RNA family
The mini-ykkC RNA motif (later renamed Guanidine-II riboswitch) was discovered as a putative RNA structure that is conserved in bacteria. The motif consists
Mini-ykkC_RNA_motif
RNA family
and sequence conservation of nhaA-I RNA Identifiers Symbol nhaA-I Rfam RF03057 Other data RNA type Cis-reg; Riboswitch SO SO:0000035 PDB structures PDBe
NhaA-I_RNA_motif
Small molecule affecting biological activity
prevents the translation of the mRNA into a protein. See also: purine riboswitch. Protein effectors An effector can also be used to refer to a protein
Effector_(biology)
Chemical compound
cyclic di-GMP. Riboswitches called the cyclic di-GMP-I riboswitch and cyclic di-GMP-II riboswitch regulate gene expression in response to cyclic di-GMP
Cyclic_di-GMP
Topics referred to by the same term
sulfurase Moco RNA motif, a conserved RNA structure presumed to be a riboswitch that binds molybdenum cofactor Moco-II RNA motif, a conserved RNA structure
Moco
American biochemist
began to look for riboswitches in nature and identified the Cobalamin riboswitch. Over the next decade, the group would perform pivotal work establishing
Ronald_Breaker
Hypothetical stage in the early evolutionary history of life on Earth
their secondary structure in response to the binding of a metabolite. Riboswitch classes have highly conserved aptamer domains, even among diverse organisms
RNA_world
Family of transport proteins
Sudarsan, N.; Breaker, R.R. (2011). "Challenges of ligand identification for riboswitch candidates". RNA Biol. 8 (1): 5–10. doi:10.4161/rna.8.1.13865. PMC 3142362
Tellurium_ion_resistance
RNA family
during genome sequencing NMT1 has been shown to act as part of a xanthane riboswitch that turns off gene expression when the ligand is bound. The NMT1 motif
NMT1_RNA_motif
Region of non-coding DNA that regulates the transcription of neighboring genes
peptide Regulates transcription of associated genes and/or operons Bacteria Riboswitch Gene regulation Bacteria, Eukaryota RNA thermometer Gene regulation Bacteria
Cis-regulatory_element
RNA family
existence of the pseudoknot is unclear. The motif does not bind as a riboswitch. Instead, it is suggested that it regulates transcription by "misincorporation"
IMPDH_RNA_motif
Structure in nucleic acids
conserved nucleotide positions, it was proposed that the motif could be a riboswitch, if it is indeed cis regulatory. Weinberg Z, Lünse CE, Corbino KA, Ames
RaiA_RNA_motif
RNA family
structure and lack of numerous conserved nucleotides is less typical of a riboswitch, and they were proposed to bind a protein. The pan RNA motif is not to
Pan_RNA_motif
RNA family
The icd-II non-coding RNA (ncRNA) is an RNA motif proposed as a Strong Riboswitch Candidate (SRC). Icd-II ncRNA has been recognized by a comparative sequence
Icd-II_ncRNA_motif
Topics referred to by the same term
transcription factors involved in limb and heart development T-box leader, a riboswitch involved in sensing tRNA aminoacylation Flaccid paralysis This disambiguation
TBOX
Class of ribonucleic acid that is not translated into proteins
genes and influence their expression in various ways. For example, a riboswitch can directly bind a small target molecule; the binding of the target affects
Non-coding_RNA
RNA family
The glucosamine-6-phosphate riboswitch ribozyme ( glmS ribozyme) is an RNA structure that resides in the 5' untranslated region (UTR) of the mRNA transcript
GlmS glucosamine-6-phosphate activated ribozyme
GlmS_glucosamine-6-phosphate_activated_ribozyme
Conserved RNA structure
2018). "Challenges of ligand identification for the second wave of orphan riboswitch candidates". RNA Biol. 15 (3): 377–390. doi:10.1080/15476286.2017.1403002
FuFi-1_RNA_motif
Three-dimensional shape of a nucleic acid polymer
essential triple helix observed in human telomerase RNA (iii) the SAM-II riboswitch and (iv) the element for nuclear expression (ENE), which acts as an RNA
Nucleic acid tertiary structure
Nucleic_acid_tertiary_structure
riboregulator in 2005 that could respond to small molecules creating a hybrid riboswitch/riboregulator molecule, termed an anti-switch. In an anti-switch, the
Riboregulator
RNA family
conserved and the queA gene itself is never known to be regulated by a preQ1 riboswitch, it is not likely that queA RNAs correspond to riboswitches. Weinberg
QueA_RNA_motif
American geneticist
Yanofsky involved collaboration with Iwona Stroynowski to reveal how a riboswitch mechanism called bacterial attenuation regulates operons for amino acid
Mitzi_Kuroda
Oligonucleotide or peptide molecules that bind specific targets
Breaker and Evgeny Nudler published the first definitive evidence for a riboswitch, a nucleic acid-based genetic regulatory element, the existence of which
Aptamer
Type of RNA molecules
metabolites and other small organic molecules, only one ribozyme based on a riboswitch has been described: glmS. Early work in characterizing self-cleaving riboswitches
Ribozyme
RNA family
was considered unusually simple compared to most (but not all) known riboswitch structures. Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth
Uup_RNA_motif
RNA family
the YybP-ykoY leader, is now known to function as a manganese-sensing riboswitch. Genes regulated by these manganese riboswitches very frequently encode
TerC_RNA_motif
RNA family
enzyme (the exact specificity of the enzyme is uncertain). A glutamine riboswitch was discovered that is often located upstream of glutamate synthase genes
GltS_RNA_motif
RNA family
leader was originally described as a conserved sequence with potential riboswitch function found upstream of the B. subtilis ykoK gene and genes with related
YkoK_leader
Conserved RNA structure
although the precise compound or set of compounds that is sensed by this riboswitch in the cell remains unclear. Weinberg Z, Wang JX, Bogue J, et al. (March
YjdF_RNA_motif
correspond to a part of a riboswitch that binds the co-factor adenosylcobalamin, which is often called the cobalamin riboswitch. (Later variants were shown
RNA_motif
Gene editing technique
degradation. Two RNA pseudoknots were tested. One was a modified prequeosine1-1 riboswitch aptamer (evopreQ1), while the other was from the Moloney murine leukemia
Prime_editing
RNA structure
structure and sequence conservation of sul1 RNA Identifiers Symbol sul1 Rfam RF03058 Other data RNA type Cis-reg; Riboswitch SO SO:0000035 PDB structures PDBe
Sul1_RNA_motif
Large self-splicing ribozymes
Group III intron Twintron LtrA Cyclic di-GMP-II riboswitch, where there is an example of a riboswitch acting together with a group I intron to regulate
Group_I_catalytic_intron
Class of enzymes
riboswitches, icd-II ncRNA motif has been proposed as a strong candidate riboswitch. Isocitrate dehydrogenase catalyzes the chemical reactions: Isocitric
Isocitrate_dehydrogenase
Medications based on ribonucleic acids
modifying the aptamer may weaken its binding affinity towards its target. Riboswitch ncRNA therapy Sahin, U.; Karikó, K.; Türeci, Ö. (2014), "mRNA-based therapeutics
RNA_therapeutics
Set of three congruent geometrical helices with the same axis
of ligand binding being influenced by a triple helix is in the SAM-II riboswitch where the triple helix creates a binding site that will uniquely accept
Triple_helix
scientists showed that the regulation mechanism of the adenine-sensing riboswitch of the human pathogenic bacterium Vibrio vulnificus is notably different
Cluster of Excellence Frankfurt Macromolecular Complexes
Cluster_of_Excellence_Frankfurt_Macromolecular_Complexes
Interactions between nucleic acid modules
cannot be referred to as true quaternary structure. Depending on where a riboswitch binds and how it is arranged, it can suppress or allow a gene to be expressed
Nucleic acid quaternary structure
Nucleic_acid_quaternary_structure
ubiquitous in all cell types and are used by all known forms of life. riboswitch A regulatory sequence within a messenger RNA transcript that can bind
Glossary of cellular and molecular biology (M–Z)
Glossary_of_cellular_and_molecular_biology_(M–Z)
Conserved RNA structure
structure and genetic experiments have led to proposals that it is a riboswitch. However, the simpler structure of the Moco-II RNA motif (see diagram)
Moco-II_RNA_motif
protein design 2004 – Cyanobacterial Circadian clock proteins 2004 – Riboswitch 2006 – Human exosome 2007 – G-protein-coupled receptor 2009 – The vault
List of biophysically important macromolecular crystal structures
List_of_biophysically_important_macromolecular_crystal_structures
RIBOSWITCH
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