Challenges of ligand identification for riboswitch candidates

Meyer, Michelle M.; Hammond, Ming C.; Salinas, Yasmmyn D.; Roth, Adam; Sudarsan, Narasimhan; Breaker, Ronald R.

doi:10.4161/rna.8.1.13865

Cited by 65 publications

(104 citation statements)

References 30 publications

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“…Experimentally validating "orphan riboswitches" whose ligands are unknown can be challenging (47,48). Therefore, establishing the ligands for the variant riboswitch candidates generated by this or other bioinformatics-based search approaches might require considerable experimental effort.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

Weinberg

Nelson

Lünse

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Riboswitches are RNAs that form complex, folded structures that selectively bind small molecules or ions. As with certain groups of protein enzymes and receptors, some riboswitch classes have evolved to change their ligand specificity. We developed a procedure to systematically analyze known riboswitch classes to find additional variants that have altered their ligand specificity. This approach uses multiple-sequence alignments, atomic-resolution structural information, and riboswitch gene associations. Among the discoveries are unique variants of the guanine riboswitch class that most tightly bind the nucleoside 2′-deoxyguanosine. In addition, we identified variants of the glycine riboswitch class that no longer recognize this amino acid, additional members of a rare flavin mononucleotide (FMN) variant class, and also variants of c-di-GMP-I and -II riboswitches that might recognize different bacterial signaling molecules. These findings further reveal the diverse molecular sensing capabilities of RNA, which highlights the potential for discovering a large number of additional natural riboswitch classes.iboswitches are structured noncoding RNA domains that regulate gene expression in response to the selective binding of small-molecule or ion ligands. The discovery of numerous classes of riboswitches has helped reveal how RNAs can form exquisitely precise ligand-binding pockets using only the four common RNA nucleotides (1-4). Furthermore, each discovery links the riboswitch ligand to the protein products of the genes under regulation. Recent riboswitch findings have exposed unique facets of biology, such as the widespread molecular mechanisms that confer fluoride (5) or guanidine (6) resistance, that maintain metal ion homeostasis (7-9), and that control important bacterial processes such as sporulation, biofilm formation, and chemotaxis (10-14). Thus, the identification of additional riboswitch classes promises to offer insights into otherwise hidden biological processes and their regulation.Riboswitch variants have been reported previously, wherein the ligand-binding "aptamer" domain has mutated to accommodate a different metabolite or signaling compound. The identification of such RNAs provides rare opportunities to study how small changes in RNA sequence can lead to major changes in smallmolecule ligand affinity. There have been seven examples, either experimentally validated or suspected, of ligand specificity changes reported to date. These include guanine aptamer variations present in riboswitches for adenine (15) and 2′-deoxyguanosine (2′-dG) (16), c-di-GMP-I aptamer variations that result in riboswitches that bind the recently discovered bacterial signaling molecule c-AMP-GMP (13, 14), and coenzyme B 12 aptamer changes (17, 18) that yield riboswitches selective for aquocobalamin (19). Three additional ligand specificity changes are suspected. Namely, some molybdenum cofactor riboswitches appear to exploit an altered aptamer structure to selectively recognize tungsten cofactor (20), certain flavin mononu...

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Section: Discussionmentioning

confidence: 99%

Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

Weinberg

Nelson

Lünse

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…One of the longest-unresolved orphan riboswitch candidates was the yybP motif RNA . After many years of uncertainty (Meyer et al 2011), both genetic (Dambach et al 2015) and structural (Price et al 2015) data eventually confirmed the hypothesis (Waters et al 2011) that members of this orphan riboswitch candidate naturally respond to Mn 2+ ions. A total of 4383 representatives of this riboswitch class have been identified in species from 18 divisions of bacteria, indicating that this riboswitch and its natural ligand are broadly important for bacteria.…”

Section: Five Distinct Riboswitch Classes Sense Atomic Ionsmentioning

confidence: 67%

“…Indeed, there are three distinct classes called guanidine-I, -II, and -III that selectively bind guanidine and regulate genes whose protein products overcome guanidine toxicity . Each of these classes, originally called ykkC ), mini-ykkC (Weinberg et al 2007), and ykkC-III was considered an orphan riboswitch candidate, with the ykkC class resisting experimental validation for over a decade (Meyer et al 2011). Guanidine-I riboswitches, for example, use a sophisticated RNA structure to form a guanidine-selective binding pocket that exploits all possible hydrogen-binding contacts and cation-π interactions with the ligand (Battaglia et al 2017;Reiss et al 2017).…”

Section: Riboswitches For Amino Acids and Other Metabolitesmentioning

confidence: 99%

Riboswitch diversity and distribution

McCown

Corbino

Stav

et al. 2017

RNA

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Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands. The research findings produced since the first riboswitch validation reports in 2002 reveal that these noncoding RNA domains exploit many different structural features to create binding pockets that are extremely selective for their target ligands. Some riboswitch classes are very common and are present in bacteria from nearly all lineages, whereas others are exceedingly rare and appear in only a few species whose DNA has been sequenced. Presented herein are the consensus sequences, structural models, and phylogenetic distributions for all validated riboswitch classes. Based on our findings, we predict that there are potentially many thousands of distinct bacterial riboswitch classes remaining to be discovered, but that the rarity of individual undiscovered classes will make it increasingly difficult to find additional examples of this RNA-based sensory and gene control mechanism.

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“…Some natural ligands had been considered to be relatively unimportant to biology, or at least were not considered by many to be important for regulating gene expression, as was the case for fluoride (Baker et al 2012) and for ZTP riboswitches. In other instances, the biochemical systems that manage the concentration of the ligand were not well established, as was the case for Mn 2+ riboswitches (Barrick et al 2004;Meyer et al 2011;Dambach et al 2015;Price et al 2015) and for all the other riboswitch ligands noted immediately above.…”

Section: Introductionmentioning

confidence: 99%

The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

Hwang

Stav

et al. 2016

RNA

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The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or "azaaromatics," trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics.

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Challenges of ligand identification for riboswitch candidates

Cited by 65 publications

References 30 publications

Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

Riboswitch diversity and distribution

The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

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