A second riboswitch class for the enzyme cofactor NAD. RNA 2021;27:99-105. [PMID: 33087526 PMCID: PMC7749635 DOI: 10.1261/rna.077891.120]

Some general principles of riboswitch structure and interactions with small-molecule ligands

Riboswitches are RNA elements with a defined structure found in noncoding sections of genes that allow the direct control of gene expression by the binding of small molecules functionally related to the gene product. In most cases, this is a metabolite in the same (typically biosynthetic) pathway as an enzyme (or transporter) encoded by the gene that is controlled. The structures of many riboswitches have been determined and this provides a large database of RNA structure and ligand binding. In this review, we extract general principles of RNA structure and the manner or ligand binding from this resource.

Inhibition of xpt Guanine Riboswitch by a synthetic nucleoside analog

Riboswitches are structured elements predominantly found in the 5'-untranslated region of many bacterial mRNA. These noncoding RNA regions play a vital role in bacterial metabolism and overall function. Each riboswitch binds to a specific small molecule and causes conformational changes in the mRNA leading to regulation of transcription or translation. In this work, we have synthesized SK4, a novel nucleoside analog that binds to the guanine riboswitch mRNA of the xanthine phosphoribosyl transferase gene in Bacillus subtilis and terminates transcription of the riboswitch mRNA to a greater extent than the native ligand guanine. Molecular dynamics simulations of SK4 with riboswitch mRNA reveal an overall stable complex with additional bonding interactions in comparison to guanine. Our work with SK4 demonstrates that specific genes in bacteria can be effectively controlled by ligand analogs, providing an alternative mechanism to regulate the function of bacteria.

Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning

Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell. Riboswitches are ubiquitous and well characterized in bacteria and prokaryotes, with additional examples also being found in fungi, plants, and yeast. To date, no purely RNA-small molecule riboswitch has been discovered in Homo Sapiens. Several analogous riboswitch-like mechanisms have been described within the H. Sapiens translatome within the past decade, prompting the question: Is there a H. Sapiens riboswitch dependent on only small molecule ligands? In this work, we set out to train positive unlabeled machine learning classifiers on known riboswitch sequences and apply the classifiers to H. Sapiens mRNA 5'UTR sequences found in the 5'UTR database, UTRdb, in the hope of identifying a set of mRNAs to investigate for riboswitch functionality. 67,683 riboswitch sequences were obtained from RNAcentral and sorted for ligand type and used as positive examples and 48,031 5'UTR sequences were used as unlabeled, unknown examples. Positive examples were sorted by ligand, and 20 positive-unlabeled classifiers were trained on sequence and secondary structure features while withholding one or two ligand classes. Cross validation was then performed on the withheld ligand sets to obtain a validation accuracy range of 75%-99%. The joint sets of 5'UTRs identified as potential riboswitches by the 20 classifiers were then analyzed. 1533 sequences were identified as a riboswitch by one or more classifier(s) and 436 of the H. Sapiens 5'UTRs were labeled as harboring potential riboswitch elements by all 20 classifiers. These 436 sequences were mapped back to the most similar riboswitches within the positive data and examined. An online database of identified and ranked 5'UTRs, their features, and their most similar matches to known riboswitches, is provided to guide future experimental efforts to identify H. Sapiens riboswitches.

DNA aptamer-based sensitive electrochemical biosensor for NAD(H) detection

Nicotinamide-adenine dinucleotide (NAD(H)) plays a critical role in cellular metabolism, and its accurate measurement is essential for elucidating biological mechanisms and disease progression. However, specific recognition probes and sensitive biosensors for NAD(H) remains a significant challenge. Here, we screen an aptamer (NAD3-1a) that exhibits specific binding to NAD(H) with micromolar affinity. By incorporating this aptamer with tetrahedral DNA nanostructure, we develop a highly selective and sensitive electrochemical biosensor for the detection of NAD(H). This biosensor enables precise detection of NAD(H) within a linear range of 10-12 ∼ 10-7 M, offering remarkable stability and reproducibility. Utilizing this biosensor, we observed significant variations in the NAD(H) levels between normal and tumor cells, as well as a notable reduction in NAD(H) in the skeletal muscle tissues of aged mice. These results highlight the potential of this aptamer-based biosensor to advance our understanding of metabolic variations in both health and disease contexts.

Development of a specific biosensor for sesquiterpene based on SELEX and directed evolution platforms

Biosensors are essential in synthetic biology, particularly for detecting compounds without distinct visual markers. In this study, a riboswitch biosensor specifically responsive to a sesquiterpene - amorpha-4,11-diene was developed for the first time. Through SELEX-SMB, a high-affinity aptamer library comprising 81,520 sequences was generated. Subsequent screening via the TBG-directed evolution platform identified riboswitch5, which downregulates downstream gene expression in response to amorpha-4,11-diene within a concentration range of 10-100 mg/L, achieving a log₂Foldchange of -0.51 at 100 mg/L. Structural predictions, combined with molecular docking and molecular dynamics simulations, revealed that ligand binding induced conformational changes that stabilize the riboswitch and enhance its repressive effect. This biosensor represents a powerful tool for the detection and regulation of small molecules, with broad applications in strain engineering, pathway regulation, and metabolic optimization in synthetic biology.

Ligand binding characteristics of an NAD+ riboswitch revealed by FRET and biolayer interferometry

The Class II NAD+ riboswitch is a bacterial RNA that binds ligands containing nicotinamide. Herein, we report a fluorescence and biolayer interferometry study of riboswitch interactions with β-NMN. The results reveal a shift in the prevalence of a pseudoknot structure in the presence of ligand and Mg2+.

An overview of engineering microbial production of nicotinamide mononucleotide

As the human body gradually ages, the cellular level of NAD+ will decline, which has been found to be related to a variety of age-related diseases. As a precursor of NAD+, NMN is able to effectively promote the synthesis of NAD+ with no significant side effects. Microbial production of NMN holds the potential to lower the production cost and facilitate its wide application. In this review, based on the metabolic pathway of NAD+, we summarize recent advances of metabolic engineering strategies for NMN biosynthesis. An outlook for future optimization to improve NMN production is also discussed.

Identification of potential riboswitch elements inHomo SapiensmRNA 5'UTR sequences using Positive-Unlabeled machine learning

Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell. Riboswitches are ubiquitous and well characterized in bacteria and prokaryotes, with additional examples also being found in fungi, plants, and yeast. To date, no purely RNA-small molecule riboswitch has been discovered in Homo Sapiens. Several analogous riboswitch-like mechanisms have been described within the H. Sapiens translatome within the past decade, prompting the question: Is there a H. Sapiens riboswitch dependent on only small molecule ligands? In this work, we set out to train positive unlabeled machine learning classifiers on known riboswitch sequences and apply the classifiers to H. Sapiens mRNA 5'UTR sequences found in the 5'UTR database, UTRdb, in the hope of identifying a set of mRNAs to investigate for riboswitch functionality. 67,683 riboswitch sequences were obtained from RNAcentral and sorted for ligand type and used as positive examples and 48,031 5'UTR sequences were used as unlabeled, unknown examples. Positive examples were sorted by ligand, and 20 positive-unlabeled classifiers were trained on sequence and secondary structure features while withholding one or two ligand classes. Cross validation was then performed on the withheld ligand sets to obtain a validation accuracy range of 75%-99%. The joint sets of 5'UTRs identified as potential riboswitches by the 20 classifiers were then analyzed. 15333 sequences were identified as a riboswitch by one or more classifier(s) and 436 of the H. Sapiens 5'UTRs were labeled as harboring potential riboswitch elements by all 20 classifiers. These 436 sequences were mapped back to the most similar riboswitches within the positive data and examined. An online database of identified and ranked 5'UTRs, their features, and their most similar matches to known riboswitches, is provided to guide future experimental efforts to identify H. Sapiens riboswitches.

Ligand binding characteristics of an NAD+ riboswitch revealed by FRET and biolayer interferometry

The Class II NAD+ riboswitch is a bacterial RNA that binds ligands containing nicotinamide. Herein, we report a fluorescence and biolayer interferometry study of riboswitch interactions with β-NMN. The results reveal a shift in the prevalence of a pseudoknot structure in the presence of ligand and Mg2+.

From bacteria to biomedicine: Developing therapies exploiting NAD+ metabolism

Nicotinamide adenine dinucleotide (NAD+) serves as a critical cofactor in cellular metabolism and redox reactions. Bacterial pathways rely on NAD+ participation, where its stability and concentration govern essential homeostasis and functions. This review delves into the role and metabolic regulation of NAD+ in bacteria, highlighting its influence on physiology and virulence. Notably, we explore enzymes linked to NAD+ metabolism as antibacterial drug targets and vaccine candidates. Moreover, we scrutinize NAD+'s medical potential, offering insights for its application in biomedicine. This comprehensive assessment informs future research directions in the dynamic realm of NAD+ and its biomedical significance.

A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine

Natural polyamines such as spermidine and spermine cations have characteristics that make them highly likely to be sensed by riboswitches, such as their general affinity to polyanionic RNA and their broad contributions to cell physiology. Despite previous claims that polyamine riboswitches exist, evidence of their biological functions has remained unconvincing. Here, we report that rare variants of bacterial S-adenosylmethionine-I (SAM-I) riboswitches reject SAM and have adapted to selectively sense spermidine. These spermidine-sensing riboswitch variants are associated with genes whose protein products are directly involved in the production of spermidine and other polyamines. Biochemical and genetic assays demonstrate that representatives of this riboswitch class robustly function as genetic "off" switches, wherein spermidine binding causes premature transcription termination to suppress the expression of polyamine biosynthetic genes. These findings confirm the existence of natural spermidine-sensing riboswitches in bacteria and expand the list of variant riboswitch classes that have adapted to bind different ligands.

Full-Length NAD+-I Riboswitches Bind a Single Cofactor but Cannot Discriminate against Adenosine Triphosphate

Bacterial riboswitches are structured RNAs that bind small metabolites to control downstream gene expression. Two riboswitch classes have been reported to sense nicotinamide adenine dinucleotide (NAD+), which plays a key redox role in cellular metabolism. The NAD+-I (class I) riboswitch stands out because it comprises two homologous, tandemly arranged domains. However, previous studies examined the isolated domains rather than the full-length riboswitch. Crystallography and ligand binding analyses led to the hypothesis that each domain senses NAD+ but with disparate equilibrium binding constants (KD) of 127 μM (domain I) and 3.4 mM (domain II). Here, we analyzed individual domains and the full-length riboswitch by isothermal titration calorimetry to quantify the cofactor affinity and specificity. Domain I senses NAD+ with a KD of 24.6 ± 8.4 μM but with a reduced ligand-to-receptor stoichiometry, consistent with nonproductive domain self-association observed by gel-filtration chromatography; domain II revealed no detectable binding. By contrast, the full-length riboswitch binds a single NAD+ with a KD of 31.5 ± 1.5 μM; dinucleotides NADH and AP2-ribavirin also bind with one-to-one stoichiometry. Unexpectedly, the full-length riboswitch also binds a single ATP equivalent (KD = 11.0 ± 3.5 μM). The affinity trend of the full-length riboswitch is ADP = ATP > NAD+ = AP2-ribavirin > NADH. Although our results support riboswitch sensing of a single NAD+ at concentrations significantly below the intracellular levels of this cofactor, our findings do not support the level of specificity expected for a riboswitch that exclusively senses NAD+. Gene regulatory implications and future challenges are discussed.

Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life

Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.

Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets

We present crystal structures of a new NAD+-binding riboswitch termed NAD+-II, bound to nicotinamide mononucleotide (NMN), nicotinamide adenine dinucleotide (NAD+) and nicotinamide riboside (NR). The RNA structure comprises a number of structural features including three helices, one of which forms a triple helix by interacting with an A5 strand in its minor-groove, and another formed from a long-range pseudoknot. The core of the structure (centrally located and coaxial with the triplex and the pseudoknot) includes two consecutive quadruple base interactions. Unusually the riboswitch binds two molecules of ligand, bound at distinct, non-overlapping sites in the RNA. Binding occurs primarily through the nicotinamide moiety of each ligand, held by specific hydrogen bonding and stacking interactions with the pyridyl ring. The mode of binding is the same for NMN, NR and the nicotinamide moiety of NAD+. In addition, when NAD+ is bound into one site it adopts an elongated conformation such that its diphosphate linker occupies a groove on the surface of the RNA, following which the adenine portion inserts into a pocket and makes specific hydrogen bonding interactions. Thus the NAD+-II riboswitch is distinct from the NAD+-I riboswitch in that it binds two molecules of ligand at separate sites, and that binding occurs principally through the nicotinamide moiety.

Discovering riboswitches: the past and the future

Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the concentrations of target ligands and regulate gene expression accordingly. In the past 20 years over 55 distinct classes of natural riboswitches have been discovered that selectively sense small molecules or elemental ions, and thousands more are predicted to exist. Evidence suggests that some riboswitches might be direct descendants of the RNA-based sensors and switches that were likely present in ancient organisms before the evolutionary emergence of proteins. We provide an overview of the current state of riboswitch research, focusing primarily on the discovery of riboswitches, and speculate on the major challenges facing researchers in the field.

Structure-based investigations of the NAD+-II riboswitch

Riboswitches are conserved non-coding domains in bacterial mRNA with gene regulation function that are essential for maintaining enzyme co-factor metabolism. Recently, the pnuC RNA motif was reported to selectively bind nicotinamide adenine dinucleotide (NAD+), defining a novel class of NAD+ riboswitches (NAD+-II) according to phylogenetic analysis. To reveal the three-dimensional architecture and the ligand-binding mode of this riboswitch, we solved the crystal structure of NAD+-II riboswitch in complex with NAD+. Strikingly and in contrast to class-I riboswitches that form a tight recognition pocket for the adenosine diphosphate (ADP) moiety of NAD+, the class-II riboswitches form a binding pocket for the nicotinamide mononucleotide (NMN) portion of NAD+ and display only unspecific interactions with the adenosine. We support this finding by an additional structure of the class-II RNA in complex with NMN alone. The structures define a novel RNA tertiary fold that was further confirmed by mutational analysis in combination with isothermal titration calorimetry (ITC), and 2-aminopurine-based fluorescence spectroscopic folding studies. Furthermore, we truncated the pnuC RNA motif to a short RNA helical scaffold with binding affinity comparable to the wild-type motif to allude to the potential of engineering the NAD+-II motif for biotechnological applications.

Genetically encoded biosensors for microbial synthetic biology: From conceptual frameworks to practical applications

Genetically encoded biosensors are the vital components of synthetic biology and metabolic engineering, as they are regarded as powerful devices for the dynamic control of genotype metabolism and evolution/screening of desirable phenotypes. This review summarized the recent advances in the construction and applications of different genetically encoded biosensors, including fluorescent protein-based biosensors, nucleic acid-based biosensors, allosteric transcription factor-based biosensors and two-component system-based biosensors. First, the construction frameworks of these biosensors were outlined. Then, the recent progress of biosensor applications in creating versatile microbial cell factories for the bioproduction of high-value chemicals was summarized. Finally, the challenges and prospects for constructing robust and sophisticated biosensors were discussed. This review provided theoretical guidance for constructing genetically encoded biosensors to create desirable microbial cell factories for sustainable bioproduction.

Insertions and deletions mediated functional divergence of Rossmann fold enzymes

Nucleobase-containing coenzymes are hypothesized to be relics of an early RNA-based world that preceded the emergence of proteins. Despite the importance of coenzyme-protein synergisms, their emergence and evolution remain understudied. An excellent target to address this issue is the Rossmann fold, the most catalytically diverse and abundant protein architecture in nature. We investigated two main Rossmann lineages: the nicotinamide adenine dinucleotide phosphate (NAD(P)) and the S-adenosyl methionine (SAM)- binding superfamilies. To identify the evolutionary changes that lead to a coenzyme specificity switch on these superfamilies, we performed structural and sequence-based Hidden Markov model analysis to systematically search for key motifs in their coenzyme-binding pockets. Our analyses revealed that through insertions and deletions (InDels) and a residue substitution, the ancient β1-loop-α1 coenzyme-binding structure of NAD(P) could be reshaped into the SAM-binding β1-loop-α1 structure. To experimentally prove this obsevation, we removed three amino acids from the NAD(P)-binding pocket and solved the structure of the resulting mutant, revealing the characteristic loop features of the SAM-binding pocket. To confirm the binding to SAM, we performed isothermal titration calorimetry measurements. Molecular dynamics simulations also corroborated the role of InDels in abolishing NAD binding and acquiring SAM binding. Our results uncovered how nature may have utilized insertions and deletions to optimize the different coenzyme-binding pockets and the distinct functionalities observed for Rossmann superfamilies. This work also proposes a general mechanism by which protein templates could have been recycled through the course of evolution to adopt different coenzymes and confer distinct chemistries.

Key players in regulatory RNA realm of bacteria

Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network.

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The three major classes of prokaryotic ncRNAs and their characterized mechanisms of operation in gene regulation.

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sRNAs emerging as major players in global gene regulatory networks.

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Riboswitch mediated gene control mechanisms through on/off switches in response to ligand binding.

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RNA thermo sensors for temperature-dependent gene expression.

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Therapeutic importance of ncRNAs and computational approaches involved in the discovery of ncRNAs.

Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine

The aptamer portions of previously reported riboswitch classes that sense guanine, adenine, or 2′-deoxyguanosine are formed by a highly similar three-stem junction with distinct nucleotide sequences in the regions joining the stems. The nucleotides in these joining regions form the major features of the selective ligand-binding pocket for each aptamer. Previously, we reported the existence of additional, rare variants of the predominant guanine-sensing riboswitch class that carry nucleotide differences in the ligand-binding pocket, suggesting that these RNAs have further diversified their structures and functions. Herein, we report the discovery and analysis of three naturally occurring variants of guanine riboswitches that are narrowly distributed across Firmicutes. These RNAs were identified using comparative sequence analysis methods, which also revealed that some of the gene associations for these variants are atypical for guanine riboswitches or their previously known natural variants. Binding assays demonstrate that the newfound variant riboswitch representatives recognize xanthine, guanine, or 2′-deoxyguanosine, with the guanine class exhibiting greater discrimination against related purines than the more common guanine riboswitch class reported previously. These three additional variant classes, together with the four previously discovered riboswitch classes that employ the same three-stem junction architecture, reveal how a simple structural framework can be diversified to expand the range of purine-based ligands sensed by RNA.

The Biochemical Landscape of Riboswitch Ligands

More than 55 distinct classes of riboswitches that respond to small metabolites or elemental ions have been experimentally validated to date. The ligands sensed by these riboswitches are biased in favor of fundamental compounds or ions that are likely to have been relevant to ancient forms of life, including those that might have populated the "RNA World", which is a proposed biochemical era that predates the evolutionary emergence of DNA and proteins. In the following text, I discuss the various types of ligands sensed by some of the most common riboswitches present in modern bacterial cells and consider implications for ancient biological processes centered on the proven capabilities of these RNA-based sensors. Although most major biochemical aspects of metabolism are represented by known riboswitch classes, there are striking sensory gaps in some key areas. These gaps could reveal weaknesses in the performance capabilities of RNA that might have hampered RNA World evolution, or these could highlight opportunities to discover additional riboswitch classes that sense essential metabolites.

DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria

SUMMARY

Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL (Discovery of Intergenic Motifs PipeLine) discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification.

AVAILABILITY AND IMPLEMENTATION

The DIMPL pipeline is freely available as a Docker image with an accompanying set of Jupyter notebooks. Full instructions for download and use are available at https://github.com/breakerlab/dimpl.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Riboswitch Mechanisms: New Tricks for an Old Dog

Discovered almost twenty years ago, riboswitches turned out to be one of the most common regulatory systems in bacteria, with representatives found in eukaryotes and archaea. Unlike many other regulatory elements, riboswitches are entirely composed of RNA and capable of modulating expression of genes by direct binding of small cellular molecules. While bacterial riboswitches had been initially thought to control production of enzymes and transporters associated with small organic molecules via feedback regulatory circuits, later findings identified riboswitches directing expression of a wide range of genes and responding to various classes of molecules, including ions, signaling molecules, and others. The 5'-untranslated mRNA regions host a vast majority of riboswitches, which modulate transcription or translation of downstream genes through conformational rearrangements in the ligand-sensing domains and adjacent expression-controlling platforms. Over years, the repertoire of regulatory mechanisms employed by riboswitches has greatly expanded; most recent studies have highlighted the importance of alternative mechanisms, such as RNA degradation, for the riboswitch-mediated genetic circuits. This review discusses the plethora of bacterial riboswitch mechanisms and illustrates how riboswitches utilize different features and approaches to elicit various regulatory responses.

Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes

Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding 'intergenic regions' (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.