PreQ1 riboswitch

Last updated
PreQ1 riboswitch
RF00522.jpg
Predicted secondary structure and sequence conservation of PreQ1
Identifiers
SymbolPreQ1
Rfam RF00522
Other data
RNA type Cis-reg; riboswitch
Domain(s) Bacteria
SO SO:0000035
PDB structures PDBe 2L1V

The PreQ1-I riboswitch is a cis-acting element identified in bacteria which regulates expression of genes involved in biosynthesis of the nucleoside queuosine (Q) from GTP. [1] PreQ1 (pre-queuosine1) is an intermediate in the 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 small aptamer, compared to other riboswitches. Its atomic-resolution three-dimensional structure has been determined, with the PDB ID 2L1V. [2] [3]

Contents

PreQ1 classification

Three subcategories of the PreQ1 riboswitch exist: preQ1-I, preQ1-II, and preQ1-III. PreQ1-I has a distinctly small aptamer, ranging from 25 to 45 nucleotides long, [4] compared to the structures of PreQ1-II riboswitch and preQ1-III riboswitch. 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. [5] PreQ1-III riboswitch has a distinct structure and is also larger in aptamer size than preQ1-I riboswitch, ranging from sizes ranging from 33 to 58 nucleotides. PreQ1-III riboswitch has an atypically organized pseudoknot that does not appear to incorporate its downstream expression platform at its ribosome binding site (RBS). [6]

History

While preQ1 was first discovered as an anticodon sequence of tRNAs from E.coli in 1972, [7] preQ1 riboswitch was not first found until 2004 [8] and recognized even later. [9] The first reported preQ1 riboswitch was located in the leader of the Bacillus subtilis ykvJKLM (queCDEF) operon which encodes four genes necessary for queuosine production. [8] In this organism, PreQ1 binding to the riboswitch aptamer is thought to induce premature transcription termination within the leader to down-regulate expression of these genes. Later on, preQ1 riboswitch was identified as a conserved sequence on the 5' UTR of genes in many gram-positive bacteria and was proved to be associated with synthesis of preQ1. [9]

In 2008, a second class of preQ1 riboswitch (PreQ1-II riboswitches) was also found as a representative of the COG4708 RNA motif from Streptococcus pneumoniae R6. [10] Although PreQ1-II riboswitch also works as queuosine biosynthetic intermediate, the structural and molecular recognition characteristics are distinct from preQ1-I riboswitch, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. [10]

Structure and function

Secondary structure of preQ1 class 1 riboswitch from Bacillus subtilis (Bsu) obtained from (PDB: 3FU2 ) using web-based RNA structure software, viennaRNA web services where P1 and P2 are the stem region, and L1, L2 and L3 are the loop region. These two stems and three loops form H-type pseudoknot in presence of preQ1. Secondary structure of preQ1 class 1 riboswitch form Bacillus subtilis (Bsu).png
Secondary structure of preQ1 class 1 riboswitch from Bacillus subtilis (Bsu) obtained from ( PDB: 3FU2 ​) using web-based RNA structure software, viennaRNA web services where P1 and P2 are the stem region, and L1, L2 and L3 are the loop region. These two stems and three loops form H-type pseudoknot in presence of preQ1.
Docking and undocking mechanism of preQ1 riboswitch in presence and absence of ligand preQ1(shown in orange). PreQ1 riboswitch docking mechanism.png
Docking and undocking mechanism of preQ1 riboswitch in presence and absence of ligand preQ1(shown in orange).
3Q51 pymol structure.png
3Q50 pymol structure.png
PreQ1 structures Left: Free structure ( PDB: 3Q51 ​) Right: Bound structure( PDB: 3Q50 ​) . Both generated by PyMOL using existing crystal structures .

PreQ1 riboswitch has two stems and three loops, and its detailed structure has been shown on the right. [11] The riboswitching action of preQ1 riboswitches in bacteria is regulated by binding of metabolite preQ1 to the aptamer region leading to structural changes in the messenger RNA (mRNA) that governs the downstream genetic regulation. [12] The preQ1 riboswitch structure adopts a compact H-type pseudoknot, which makes it quite different from other purine based riboswitches. [12] The preQ1 ligand is buried in the pseudoknot core and stabilized through intercalation between helical stacks and hydrogen bond interaction with heteroatoms. In absence of preQ1, the P2 tail region is away from the P2 loop region and hence the riboswitch is observed to be in undocked (partially docked) state, whereas on the binding of preQ1 to the riboswitch results the two P2 regions to come closer causing a complete docking of riboswitch. This docking and undocking mechanism of riboswitch with the change in concentration of ligand preQ1 is observed to control the signaling of gene regulation, commonly known as “ON” or “OFF” signaling for gene expression. [11] [13] The docking and undocking mechanism are observed to be affected not only by the ligand, but also with other factors like Mg salt. [14] Like any other riboswitch, the two most common types of gene regulation mediated by preQ1 riboswitch are through transcription attenuation or inhibition of translation initiation. Ligand binding to the transcriptional riboswitch in bacterial causes modification in the structure of riboswitch unit, which leads to hindrance in the activity of RNA polymerase causing attenuation of transcription. Similarly, binding of the ligand to the translational riboswitch causes modification in the secondary structure of riboswitch unit leading to hindrance for ribosome binding and hence inhibiting translational initiation.

Transcriptional regulation

PreQ1 mediated transcriptional attenuation is controlled by the dynamic switching of anti-terminator and terminator hairpin in the riboswitch. [11] For preQ1 riboswitch from bacteria Bacillus subtilis (Bsu), the anti-terminator is predicted to be less stable than the terminator, as the addition of preQ1 shifts the equilibrium significantly towards the formation of terminator. [11] In presence of preQ1, the 3’ end of the adenine rich tail domain pairs with the center of P1 hairpin loop to form an H-type pseudoknot. [11] In the native mRNA structure, binding of preQ1 to the aptamer region in the riboswitch leads to the formation of a terminator hairpin which causes RNA polymerase to stop transcription, a process which is commonly known as OFF- regulation of genetic expression or transcription termination. [13]

Translation regulation

Translation of protein in prokaryotes is initiated by binding of 30S ribosomal subunit to the Shine-Dalgarno (SD) sequence in mRNA. PreQ1 mediated inhibition of translational regulation is controlled by blocking the Shine-Dalgarno sequence of mRNA to prevent binding of ribosome to mRNA for translation. Binding of preQ1 to the aptamer domain promotes the sequestration of a part of SD sequence at the 5’ end to the P2 stem of the aptamer domain causing inaccessibility of the SD sequence. [11] The translational riboswitch from bacteria Thermoanaerobacter tengcongensis (Tte) is observed to be transiently closed (pre-docked) in absence of preQ1, whereas in presence of preQ1 a fully docked state is adopted. This docking/undocking equilibrium is not only regulated by the concentration of ligand but also by the concentration of Mg salt. [14] [15] The unavailability of SD sequence due to the formation of pseudoknot in presence of preQ1 shows the OFF-regulation of genetic expression in translational riboswitch or inhibition of translational initiation.

Physiological relevance in bacterial gene regulation

PreQ1 riboswitch activity in Tte bacteria can be measured by the levels of two proteins that are in the coding region of the Tte mRNA, which are TTE1564 and TTE1563. [16] Proteins downstream of the preQ1 riboswitch biosynthesize a nucleobase called queuine and a nucleoside queuosine are inhibited by the activation of the preQ1 riboswitch. Queuine is involved in the anticodon sequence of certain tRNA. [17] In bacteria, the hyper-modified nucleobase queuine takes up the first anticodon position, or its wobble position in the tRNA of asparagine, aspartic acid, histidine, and tyrosine. [18] In bacteria the enzyme tRNA-guanine transglycosylase (TGT) catalyzes the swap of a guanine in position 34 of the tRNA with queuine into the first anitcodon position. [15] [16] Eukaryae incorporate queuine into RNA, whereas eubacteria incorporate preQ1, which then undergoes modification to yield queuine. [17] Since queuosine is exclusively produced in bacteria, eukaryotic organisms must obtain their supply of queuosine or its nucleobase queuine from their diet or bacteria from their gut microflora. The implication of a deficiency of queuine or queuosine is an inability to make queuosine-modified tRNA, and furthermore, the inability of the cell to convert phenylalanine to tyrosine. [19]

See also

Related Research Articles

<span class="mw-page-title-main">Riboswitch</span>

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 of the proteins 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 proteins, catalyze reactions, or to bind other RNA or protein macromolecules.

<span class="mw-page-title-main">Cobalamin riboswitch</span>

Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' untranslated regions of vitamin B12 (Cobalamin) related genes in bacteria.

<span class="mw-page-title-main">FMN riboswitch</span> Highly conserved RNA element

The FMN riboswitch 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 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. In Bacillus subtilis, previous studies have shown that this bacterium utilizes at least two FMN riboswitches, where one controls translation initiation, and the other controls premature transcription termination. Regarding the second riboswitch in Bacilius subtilis, premature transcription termination occurs within the 5' untranslated region of the ribDEAHT operon, precluding access to the ribosome-binding site of ypaA mRNA. FMN riboswitches also have various magnesium and potassium ions dispersed throughout the nucleotide structure, some of which participate in binding of FMN.

<span class="mw-page-title-main">Glycine riboswitch</span> 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 aptamer domains with similar structures in tandem. The aptamers were originally thought to cooperatively bind glycine to regulate the expression of downstream genes. In Bacillus subtilis, this riboswitch is found upstream of the gcvT operon which controls glycine degradation. It is thought that when glycine is in excess it will bind to both aptamers to activate these genes and facilitate glycine degradation.

<span class="mw-page-title-main">Lysine riboswitch</span>

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. The lysine riboswitch has also been identified independently and called the L box.

<span class="mw-page-title-main">Purine riboswitch</span>

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 revealing an expression platform for a downstream gene, or by forming a translation-terminating stem-loop. The ultimate effects of such translational regulation often take action to manage an abundance of the instigating purine, and might produce proteins that facilitate purine metabolism or purine membrane uptake.

<span class="mw-page-title-main">SAM-II riboswitch</span>

The SAM-II riboswitch is an RNA element found predominantly in Alphaproteobacteria that binds S-adenosyl methionine (SAM). Its structure and sequence appear to be unrelated to the SAM riboswitch found in Gram-positive bacteria. This SAM riboswitch is located upstream of the metA and metC genes in Agrobacterium tumefaciens, and other methionine and SAM biosynthesis genes in other alpha-proteobacteria. Like the other SAM riboswitch, it probably functions to turn off expression of these genes in response to elevated SAM levels. A significant variant of SAM-II riboswitches was found in Pelagibacter ubique and related marine bacteria and called SAM-V. Also, like many structured RNAs, SAM-II riboswitches can tolerate long loops between their stems.

<span class="mw-page-title-main">SAM riboswitch (S-box leader)</span>

The SAM riboswitch is found upstream of a number of genes which code for proteins involved in methionine or cysteine biosynthesis in Gram-positive bacteria. Two SAM riboswitches in Bacillus subtilis that were experimentally studied act at the level of transcription termination control. The predicted secondary structure consists of a complex stem-loop region followed by a single stem-loop terminator region. An alternative and mutually exclusive form involves bases in the 3' segment of helix 1 with those in the 5' region of helix 5 to form a structure termed the anti-terminator form. When SAM is unbound, the anti-terminator sequence sequesters the terminator sequence so the terminator is unable to form, allowing the polymerase to read-through the downstream gene. When S-Adenosyl methionine (SAM) is bound to the aptamer, the anti-terminator is sequestered by an anti-anti-terminator; the terminator forms and terminates the transcription. However, many SAM riboswitches are likely to regulate gene expression at the level of translation.

ykkC-yxkD leader Conserved RNA structure in bacteria

The ykkC/yxkD leader is a conserved RNA structure found upstream of the ykkC and yxkD genes in Bacillus subtilis and related genes in other bacteria. The function of this family is unclear for many years although it has been suggested that it may function to switch on efflux pumps and detoxification systems in response to harmful environmental molecules. The Thermoanaerobacter tengcongensis sequence AE013027 overlaps with that of purine riboswitch suggesting that the two riboswitches may work in conjunction to regulate the upstream gene which codes for TTE0584 (Q8RC62), a member of the permease family.

<span class="mw-page-title-main">PreQ1-II riboswitch</span> Class of riboswitches

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 identified as a conserved RNA secondary structure called the "COG4708 motif". All known members of this riboswitch class appear to control members of COG4708 genes. These genes are predicted to encode membrane-bound proteins and have been proposed to be a transporter of preQ1, or a related metabolite, based on their association with preQ1-binding riboswitches. PreQ1-II riboswitches have no apparent similarities in sequence or structure to preQ1-I riboswitches, a previously discovered class of preQ1-binding riboswitches. PreQ1 thus joins S-adenosylmethionine as the second metabolite to be found that is the ligand of more than one riboswitch class.

<span class="mw-page-title-main">Queuosine</span> Chemical compound

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 histidine, aspartic acid, asparagine and tyrosine. The first anticodon position pairs with the third "wobble" position in codons, and queuosine improves accuracy of translation compared to guanosine. Synthesis of queuosine begins with GTP. In bacteria, three structurally unrelated classes of riboswitch are known to regulate genes that are involved in the synthesis or transport of pre-queuosine1, a precursor to queuosine: PreQ1-I riboswitches, PreQ1-II riboswitches and PreQ1-III riboswitches.

<span class="mw-page-title-main">SAM-IV riboswitch</span>

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 Actinomycetales, an order of Bacteria. Conserved features of SAM-IV riboswitch and experiments imply that they probably share a similar SAM-binding site to another class of SAM-binding riboswitches called SAM-I riboswitches. However, the scaffolds of these two types of riboswitch appear to be quite distinct. The structural relationship between these riboswitch types has been studied.

The Magnesium 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 transporter protein MgtA. It is located in the 5' UTR of this gene. The mechanism for the potential magnesium-sensing capacity of this RNA is still unclear, though 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.

<span class="mw-page-title-main">Mesoplasma florum riboswitch</span>

Riboswitches are cis-acting regulatory elements located within the 5’UTR of mRNA transcripts. These regulatory elements bind small molecules which results in a conformational change within the 5’UTR of the mRNA. The changes in the mRNA secondary structure subsequently result in changes in the expression of the adjacent open reading frame.

<span class="mw-page-title-main">SAM–SAH riboswitch</span> 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 presumed to be a riboswitch. SAM–SAH riboswitches do not share any apparent structural resemblance to known riboswitches that bind SAM or SAH. The binding affinities for both compounds are similar, but binding for SAH is at least somewhat stronger. SAM–SAH riboswitches are exclusively found in Rhodobacterales, an order of alphaproteobacteria. They are always found in the apparent 5' untranslated regions of metK genes, which encode the enzyme that synthesizes SAM.

<span class="mw-page-title-main">Fluoride riboswitch</span> Fluoride-binding RNA structure

The fluoride riboswitch 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.

<span class="mw-page-title-main">Glutamine riboswitch</span> Glutamine-binding RNA structure

The glutamine riboswitch is a conserved RNA structure that was predicted by bioinformatics. 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.

<span class="mw-page-title-main">Tetrahydrofolate riboswitch</span> Class of homologous RNAs

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 known to encode either folate transporters or enzymes involved in folate metabolism. For these reasons it was inferred that the RNAs function as riboswitches. THF riboswitches are found in a variety of Bacillota, specifically the orders Clostridiales and 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 genomics. The 3-d structure of the tetrahydrofolate riboswitch has been solved by separate groups using X-ray crystallography. These structures were deposited into the Protein Data Bank under accessions 3SD1 and 3SUX, with other entries containing variants.

SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine (SAM). It was first discovered in the marine bacterium Candidatus Pelagibacter ubique and can also be found in marine metagenomes. SAM-V features a similar consensus sequence and secondary structure as the binding site of SAM-II riboswitch, but bioinformatics scans cluster the two aptamers independently. These similar binding pockets suggest that the two riboswitches have undergone convergent evolution.

<span class="mw-page-title-main">PreQ1-III riboswitch</span>

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 structurally distinct from preQ1-I and preQ1-II riboswitches. Most sequenced examples of preQ1-III riboswitches are obtained from uncultivated metagenome samples, but the few examples in cultivated organisms are present in strains that are known to or suspected to be Faecalibacterium prausnitzii, a species of Gram-positive Clostridia. Known examples of preQ1-III riboswitches are found upstream of queT genes, which are expected to encode transporters of a queuosine derivative. The other two known classes of preQ1 riboswitches are also commonly found upstream of queT genes.

References

  1. ↑ Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR (2007). "A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain". Nat Struct Mol Biol. 14 (4): 308–317. doi:10.1038/nsmb1224. PMID   17384645. S2CID   32367656.
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  19. ↑ Rakovich, Tatsiana; Boland, Coilin; Bernstein, Ilana; Chikwana, Vimbai M.; Iwata-Reuyl, Dirk; Kelly, Vincent P. (2011-06-03). "Queuosine Deficiency in Eukaryotes Compromises Tyrosine Production through Increased Tetrahydrobiopterin Oxidation". Journal of Biological Chemistry. 286 (22): 19354–19363. doi: 10.1074/jbc.M111.219576 . ISSN   0021-9258. PMC   3103313 . PMID   21487017.
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