Genetic control by a metabolite binding mRNA

Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology

Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.

Coenzymes and Their Role in the Evolution of Life

The evolution of coenzymes, or their impact on the origin of life, is fundamental for understanding our own existence. Having established reasonable hypotheses about the emergence of prebiotic chemical building blocks, which were probably created under palaeogeochemical conditions, and surmising that these smaller compounds must have become integrated to afford complex macromolecules such as RNA, the question of coenzyme origin and its relation to the evolution of functional biochemistry should gain new impetus. Many coenzymes have a simple chemical structure and are often nucleotide-derived, which suggests that they may have coexisted with the emergence of RNA and may have played a pivotal role in early metabolism. Based on current theories of prebiotic evolution, which attempt to explain the emergence of privileged organic building blocks, this Review discusses plausible hypotheses on the prebiotic formation of key elements within selected extant coenzymes. In combination with prebiotic RNA, coenzymes may have dramatically broadened early protometabolic networks and the catalytic scope of RNA during the evolution of life.

Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics

Background

Only 1.5% of the human genome encodes proteins, while large part of the remaining encodes noncoding RNAs (ncRNA). Many ncRNAs form structures and perform many important functions. Accurately identifying structured ncRNAs in the human genome and discovering their biological functions remain a major challenge.

Results

Here, we have established a pipeline (CM-line) with the following features for analyzing the large genomes of humans and other animals. First, we selected species with larger genetic distances to facilitate the discovery of covariations and compatible mutations. Second, we used CMfinder, which can generate useful alignments even with low sequence conservation. Third, we removed repetitive sequences and known structured ncRNAs to reduce the workload of CMfinder. Fourth, we used Infernal to find more representatives and refine the structure. We reported 11 classes of structured ncRNA candidates with significant covariations in humans. Functional analysis showed that these ncRNAs may have variable functions. Some may regulate circadian clock genes through poly (A) signals (PAS); some may regulate the elongation factor (EEF1A) and the T-cell receptor signaling pathway by cooperating with RNA binding proteins.

Conclusions

By searching for important features of RNA structure from large genomes, the CM-line has revealed the existence of a variety of novel structured ncRNAs. Functional analysis suggests that some newly discovered ncRNA motifs may have biological functions. The pipeline we have established for the discovery of structured ncRNAs and the identification of their functions can also be applied to analyze other large genomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07474-9.

Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing

Oligonucleotide receptors (aptamers), which change conformation upon target recognition, enable electronic biosensing under high ionic-strength conditions when coupled to field-effect transistors (FETs). Because highly negatively charged aptamer backbones are influenced by ion content and concentration, biosensor performance and target sensitivities were evaluated under application conditions. For a recently identified dopamine aptamer, physiological concentrations of Mg²⁺ and Ca²⁺ in artificial cerebrospinal fluid produced marked potentiation of dopamine FET-sensor responses. By comparison, divalent cation-associated signal amplification was not observed for FET sensors functionalized with a recently identified serotonin aptamer or a previously reported dopamine aptamer. Circular dichroism spectroscopy revealed Mg²⁺- and Ca²⁺-induced changes in target-associated secondary structure for the new dopamine aptamer, but not the serotonin aptamer nor the old dopamine aptamer. Thioflavin T displacement corroborated the Mg²⁺ dependence of the new dopamine aptamer for target detection. These findings imply allosteric binding interactions between divalent cations and dopamine for the new dopamine aptamer. Developing and testing sensors in ionic environments that reflect intended applications are best practices for identifying aptamer candidates with favorable attributes and elucidating sensing mechanisms.

Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch

We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.

The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding

The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.

Riboswitch theo/metE as a Transcription Regulation Tool for Xanthomonas citri subsp. citri

: Xanthomonas citri subsp. citri (X. citri) is the causal agent of Asiatic Citrus Canker (ACC), a disease that affects citrus. ACC has no cure, and growers must rely on special agricultural practices to prevent bacterial spreading. Understanding X. citri basic biology is essential to foresee potential genetic targets to control ACC. Traditionally, microbial genetics use gene deletion/disruption to investigate gene function. However, essential genes are difficult to study this way. Techniques based on small-RNAs and antisense-RNAs are powerful for gene characterization, but not yet fully explored in prokaryotes. One alternative is riboswitches, which derive from bacteria, and can control transcription/translation. Riboswitches are non-coding RNAs able to modulate gene expression in the presence of specific ligands. Here we demonstrate that the riboswitch theo/metE decreases parB expression in X. citri in a platform responsive to theophylline. By monitoring cell respiration, we showed that higher concentrations of the ligand interfered with bacterial viability. Therefore, we determined the safe dose of theophylline to be used with X. citri. Finally, in downstream investigations of parB transcription modulation, we show evidence for the fact that ParB is stable, remains functional throughout the cell cycle, and is inherited by the daughter cells upon cell division.

Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences

The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.

Discovery and characterization of a fourth class of guanidine riboswitches

Riboswitches are RNAs that specifically sense a small molecule and regulate genes accordingly. The recent discovery of guanidine-binding riboswitches revealed the biological significance of this compound, and uncovered genes related to its biology. For example, certain sugE genes encode guanidine exporters and are activated by the riboswitches to reduce toxic levels of guanidine in the cell. In order to study guanidine biology and riboswitches, we applied a bioinformatics strategy for discovering additional guanidine riboswitches by searching for new candidate motifs associated with sugE genes. Based on in vitro and in vivo experiments, we determined that one of our six best candidates is a new structural class of guanidine riboswitches. The expression of a genetic reporter was induced 80-fold in response to addition of 5 mM guanidine in Staphylococcus aureus. This new class, called the guanidine-IV riboswitch, reveals additional guanidine-associated protein domains that are extremely rarely or never associated with previously established guanidine riboswitches. Among these protein domains are two transporter families that are structurally distinct from SugE, and could represent novel types of guanidine exporters. These results establish a new metabolite-binding RNA, further validate a bioinformatics method for finding riboswitches and suggest substrate specificities for as-yet uncharacterized transporter proteins.

A single small molecule fluorescent probe for imaging RNA distribution and detecting endogenous SO2 through distinct fluorescence channels

Herein, we developed a novel small molecule fluorescent probe for imaging the distribution of RNA and detecting endogenous SO2 through distinct fluorescence channels in cells.

The requirement for cobalt in vitamin B12: A paradigm for protein metalation

Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.

Frameworks for targeting RNA with small molecules

Since the characterization of mRNA in 1961, our understanding of the roles of RNA molecules has significantly grown. Beyond serving as a link between DNA and proteins, RNA molecules play direct effector roles by binding to various ligands, including proteins, DNA, other RNAs, and metabolites. Through these interactions, RNAs mediate cellular processes such as the regulation of gene transcription and the enhancement or inhibition of protein activity. As a result, the misregulation of RNA molecules is often associated with disease phenotypes, and RNA molecules have been increasingly recognized as potential targets for drug development efforts, which in the past had focused primarily on proteins. Although both small molecule-based and oligonucleotide-based therapies have been pursued in efforts to target RNA, small-molecule modalities are often favored owing to several advantages including greater oral bioavailability. In this review, we discuss three general frameworks (sets of premises and hypotheses) that, in our view, have so far dominated the discovery of small-molecule ligands for RNA. We highlight the unique merits of each framework as well as the pitfalls associated with exclusive focus of ligand discovery efforts within only one framework. Finally, we propose that RNA ligand discovery can benefit from using progress made within these three frameworks to move toward a paradigm that formulates RNA-targeting questions at the level of RNA structural subclasses.

Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding

Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD⁺). The second domain which comprises the ribosomal binding site in a putative regulatory helix, however, has withdrawn from detection of ligand-induced structural modulation thus far, and therefore, the identity of the cognate ligand and the regulation mechanism have remained unclear. Here, we report crystal structures of both riboswitch domains, each bound to NAD⁺. Furthermore, we demonstrate that ligand binding to domain 2 requires significantly higher concentrations of NAD⁺ (or ADP retaining analogs) compared to domain 1. Using a fluorescence spectroscopic approach, we further shed light on the structural features which are responsible for the different ligand affinities, and describe the Mg²⁺-dependent, distinct folding and pre-organization of their binding pockets. Finally, we speculate about possible scenarios for nadA RNA gene regulation as a putative two-concentration sensor module for a time-controlled signal that is primed and stalled by the gene regulation machinery at low ligand concentrations (domain 1), and finally triggers repression of translation as soon as high ligand concentrations are reached in the cell (domain 2).

Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea

In prokaryotes, the key players in transcription initiation are sigma factors and transcription factors that bind to DNA to modulate the process, while premature transcription termination at the 5' end of the genes is regulated by attenuation and, in particular, by attenuation associated with riboswitches. In this study, we describe the distribution of these regulators across phylogenetic groups of bacteria and archaea and find that their abundance not only depends on the genome size, as previously described, but also varies according to the phylogeny of the organism. Furthermore, we observed a tendency for organisms to compensate for the low frequencies of a particular type of regulatory element (i.e., transcription factors) with a high frequency of other types of regulatory elements (i.e., sigma factors). This study provides a comprehensive description of the more abundant COG, KEGG, and Rfam families of transcriptional regulators present in prokaryotic genomes.IMPORTANCE In this study, we analyzed the relationship between the relative frequencies of the primary regulatory elements in bacteria and archaea, namely, transcription factors, sigma factors, and riboswitches. In bacteria, we reveal a compensatory behavior for transcription factors and sigma factors, meaning that in phylogenetic groups in which the relative number of transcription factors was low, we found a tendency for the number of sigma factors to be high and vice versa. For most of the phylogenetic groups analyzed here, except for Firmicutes and Tenericutes, a clear relationship with other mechanisms was not detected for transcriptional riboswitches, suggesting that their low frequency in most genomes does not constitute a significant impact on the global variety of transcriptional regulatory elements in prokaryotic organisms.

The computational approaches of lncRNA identification based on coding potential: Status quo and challenges

Long noncoding RNAs (lncRNAs) make up a large proportion of transcriptome in eukaryotes, and have been revealed with many regulatory functions in various biological processes. When studying lncRNAs, the first step is to accurately and specifically distinguish them from the colossal transcriptome data with complicated composition, which contains mRNAs, lncRNAs, small RNAs and their primary transcripts. In the face of such a huge and progressively expanding transcriptome data, the in-silico approaches provide a practicable scheme for effectively and rapidly filtering out lncRNA targets, using machine learning and probability statistics. In this review, we mainly discussed the characteristics of algorithms and features on currently developed approaches. We also outlined the traits of some state-of-the-art tools for ease of operation. Finally, we pointed out the underlying challenges in lncRNA identification with the advent of new experimental data.

RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges

RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.

Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD⁺, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.

Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth

The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA enzymes from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support. Long polymers, with maximum lengths sometimes exceeding 100 nucleotides, spontaneously emerge due to a combination of non-enzymatic, non-templated polymer extension and template-directed primer extension processes. The former helps in increasing the lengths of RNA strands, whereas the later helps in producing complementary copies of the strands. Strands also undergo hydrolysis in a structure-dependent manner that favour breaking of bonds connecting unpaired nucleotides. We identify the most favourable conditions needed for the emergence of ribozyme and tRNA-like structures and double stranded RNA molecules, classify all RNA strands on the basis of their secondary structures and determine their abundance in the population. Our results indicate that under suitable environmental conditions, non-enzymatic processes would have been sufficient to lead to the emergence of a variety of ribozyme-like molecules with complex secondary structures and potential catalytic functions.

Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding

Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.

Sharing vitamins: Cobamides unveil microbial interactions

Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B₁₂), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.

Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy

Riboswitches are cis-regulatory genetic elements that use an aptamer to control gene expression. Specificity to cognate ligand and diversity of such ligands have expanded the functional repertoire of riboswitches to mediate mounting apt responses to sudden metabolic demands and signal changes in environmental conditions. Given their critical role in microbial life, riboswitch characterisation remains a challenging computational problem. Here we have addressed the issue with advanced deep learning frameworks, namely convolutional neural networks (CNN), and bidirectional recurrent neural networks (RNN) with Long Short-Term Memory (LSTM). Using a comprehensive dataset of 32 ligand classes and a stratified train-validate-test approach, we demonstrated the accurate performance of both the deep learning models (CNN and RNN) relative to conventional hyperparameter-optimized machine learning classifiers on all key performance metrics, including the ROC curve analysis. In particular, the bidirectional LSTM RNN emerged as the best-performing learning method for identifying the ligand-specificity of riboswitches with an accuracy >0.99 and macro-averaged F-score of 0.96. An additional attraction is that the deep learning models do not require prior feature engineering. A dynamic update functionality is built into the models to factor for the constant discovery of new riboswitches, and extend the predictive modeling to new classes. Our work would enable the design of genetic circuits with custom-tuned riboswitch aptamers that would effect precise translational control in synthetic biology. The associated software is available as an open-source Python package and standalone resource for use in genome annotation, synthetic biology, and biotechnology workflows.

Photocaged functional nucleic acids for spatiotemporal imaging in biology

Imaging of species in living organisms with high spatiotemporal resolution is essential for understanding biological processes. While functional nucleic acids (FNAs), such as catalytic nucleic acids and aptamers, have emerged as effective sensors for a wide range of molecules, photocaged control of these FNAs has played a key role in translating them into bioimaging agents with high spatiotemporal control. In this review, we summarize methods and results of photocaged FNAs based on photolabile modifications, photoisomerization, and photothermal activation. Future directions, including strategies to improve the performance of these photocaged FNAs, are also described.

A SAM-I riboswitch with the ability to sense and respond to uncharged initiator tRNA

All known riboswitches use their aptamer to senese one metabolite signal and their expression platform to regulate gene expression. Here, we characterize a SAM-I riboswitch (SAM-I_Xcc) from the Xanthomonas campestris that regulates methionine synthesis via the met operon. In vitro and in vivo experiments show that SAM-I_Xcc controls the met operon primarily at the translational level in response to cellular S-adenosylmethionine (SAM) levels. Biochemical and genetic data demonstrate that SAM-I_Xcc expression platform not only can repress gene expression in response to SAM binding to SAM-I_Xcc aptamer but also can sense and bind uncharged initiator Met tRNA, resulting in the sequestering of the anti-Shine-Dalgarno (SD) sequence and freeing the SD for translation initiation. These findings identify a SAM-I riboswitch with a dual functioning expression platform that regulates methionine synthesis through a previously unrecognized mechanism and discover a natural tRNA-sensing RNA element. This SAM-I riboswitch appears to be highly conserved in Xanthomonas species.

Riboswitches consist of an aptamer domain and expression platform, which senses a signal and regulates gene expression, respectively. Here the authors show that the expression platform of a SAM-I riboswitch from the Gram-negative bacteria can sense and bind uncharged an initiator Met tRNA to control the met operon.

Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes

Comparative sequence analyses have been used to discover numerous classes of structured noncoding RNAs, some of which are riboswitches that specifically recognize small-molecule or elemental ion ligands and influence expression of adjacent downstream genes. Determining the correct identity of the ligand for a riboswitch candidate typically is aided by an understanding of the genes under its regulatory control. Riboswitches whose ligands were straightforward to identify have largely been associated with well-characterized metabolic pathways, such as coenzyme or amino acid biosynthesis. Riboswitch candidates whose ligands resist identification, collectively known as orphan riboswitches, are often associated with genes coding for proteins of unknown function, or genes for various proteins with no established link to one another. The cognate ligands for 16 former orphan riboswitch motifs have been identified to date. The successful pursuit of the ligands for these classes has provided insight into areas of biology that are not yet fully explored, such as ion homeostasis, signaling networks, and other previously underappreciated biochemical or physiological processes. Herein we discuss the strategies and methods used to match ligands with orphan riboswitch classes, and overview the lessons learned to inform and motivate ongoing efforts to identify ligands for the many remaining candidates.

Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria

Non-coding RNAs play pivotal roles in bacterial signaling. However, RNAs from certain phyla (specially high-GC actinobacteria) still remain elusive. Here, by re-engineering the existing genome-wide search approach, we discover a family of structurally conserved RNAs that are present ubiquitously across actinobacteria, including mycobacteria. In vitro analysis shows that RNAs belonging to this family bind response-regulator proteins that contain the widely prevalent ANTAR domain. The Mycobacterium tuberculosis ANTAR protein gets phosphorylated by a histidine kinase and interacts with RNA only in its phosphorylated state. These newly identified RNAs reside only in certain transcripts and typically overlap with the ribosome-binding site, regulating translation of these transcripts. In this way, the RNAs directly link signaling pathways to translational control, thus expanding the mechanistic tool kit available for ANTAR-based control of gene expression. In mycobacteria, we find that RNAs targeted by ANTAR proteins majorly encode enzymes of lipid metabolism and associated redox pathways. This now allows us to identify the key genes that mediate ANTAR-dependent control of lipid metabolism. Our study establishes the identity and wide prevalence of ANTAR-target RNAs in mycobacteria, bringing RNA-mediated regulation in these bacteria to the center stage.

Signaling Aptamer Optimization through Selection Using RNA-Capturing Microsphere Particles

An RNA signaling aptamer is composed of two units: a sensing aptamer that binds the input target molecule and a working aptamer that binds the output target molecule to result in a detectable signal. A conformational change of the signaling aptamer that induces an allosteric interaction with the output target molecule in response to the input target molecule depends on a junction region, which connects the two aptamer units. Efficient and effective optimization of the junction region remains a technical challenge. In this study, we demonstrate a simple strategy for optimizing the junction region through functional RNA selection using RNA-capturing microsphere particles. From approximately 0.2 million sequence variants, a signaling aptamer that enabled intracellular detection of S-adenosyl methionine with a high signal-to-noise ratio, which is approximately 2-fold higher relative fluorescence increment compared to the previously reported signaling aptamer, was obtained after single round of selection. The technology demonstrated here can be used to select RNA sequences that carry out specific functions in response to particular stimuli.

Biological Materials: The Next Frontier for Cell-Free Synthetic Biology

Advancements in cell-free synthetic biology are enabling innovations in sustainable biomanufacturing, that may ultimately shift the global manufacturing paradigm toward localized and ecologically harmonized production processes. Cell-free synthetic biology strategies have been developed for the bioproduction of fine chemicals, biofuels and biological materials. Cell-free workflows typically utilize combinations of purified enzymes, cell extracts for biotransformation or cell-free protein synthesis reactions, to assemble and characterize biosynthetic pathways. Importantly, cell-free reactions can combine the advantages of chemical engineering with metabolic engineering, through the direct addition of co-factors, substrates and chemicals -including those that are cytotoxic. Cell-free synthetic biology is also amenable to automatable design cycles through which an array of biological materials and their underpinning biosynthetic pathways can be tested and optimized in parallel. Whilst challenges still remain, recent convergences between the materials sciences and these advancements in cell-free synthetic biology enable new frontiers for materials research.

Exception to the exception rule: synthetic and naturally occurring single chromosome Vibrio cholerae

The genome of Vibrio cholerae, the etiological agent of cholera, is an exception to the single chromosome rule found in the vast majority of bacteria and has its genome partitioned between two unequally sized chromosomes. This unusual two-chromosome arrangement in V. cholerae has sparked considerable research interest since its discovery. It was demonstrated that the two chromosomes could be fused by deliberate genome engineering or forced to fuse spontaneously by blocking the replication of Chr2, the secondary chromosome. Recently, natural isolates of V. cholerae with chromosomal fusion have been found. Here, we summarize the pertinent findings on this exception to the exception rule and discuss the potential utility of single-chromosome V. cholerae to address fundamental questions on chromosome biology in general and DNA replication in particular.

Computational study of switching mechanism in add A-riboswitch

Riboswitch can bind small molecules to regulate gene expression. Unlike other RNAs, riboswitch relies on its conformational switching for regulation. However, the understanding of the switching mechanism is still limited. Here, we focussed on the add A-riboswitch to illustrate the dynamical switching mechanism as an example. We performed molecular dynamics simulation, conservation and co-evolution calculations to infer the dynamical motions and evolutionary base pairings. The results suggest that the binding domain is stable for molecule recognition and binding, whereas the switching base pairings are co-evolutionary for translation. The understanding of the add A-riboswitch switching mechanism provides a potential solution for riboswitch drug design.

Development of a new oligonucleotide block location-based feature extraction (BLBFE) method for the classification of riboswitches

As knowledge of genetics and genome elements increases, the demand for the development of bioinformatics tools for analyzing these data is raised. Riboswitches are genetic components, usually located in the untranslated regions of mRNAs, that regulate gene expression. Additionally, their interaction with antibiotics has been recently suggested, implying a role in antibiotic effects and resistance. Following a previously published sequential block finding algorithm, herein, we report the development of a new block location-based feature extraction strategy (BLBFE). This procedure utilizes the locations of family-specific sequential blocks on riboswitch sequences as features. Furthermore, the performance of other feature extraction strategies, including mono- and dinucleotide frequencies, k-mer, DAC, DCC, DACC, PC-PseDNC-General and SC-PseDNC-General methods, was investigated. KNN, LDA, naïve Bayes, PNN and decision tree classifiers accompanied by V-fold cross-validation were applied for all methods of feature extraction, and their performances based on the defined feature extraction strategies were compared. Performance measures of accuracy, sensitivity, specificity and F-score for each method of feature extraction were studied. The proposed feature extraction strategy resulted in classification of riboswitches with an average correct classification rate (CCR) of 90.8%. Furthermore, the obtained data confirmed the performance of the developed feature extraction method with an average accuracy of 96.1%, an average sensitivity of 90.8%, an average specificity of 97.52% and an average F-score of 90.69%. Our results implied that the proposed feature extraction (BLBFE) method can classify and discriminate riboswitch families with high CCR, accuracy, sensitivity, specificity and F-score values.

Flexible Cobamide Metabolism in Clostridioides (Clostridium) difficile 630 Δerm

Clostridioides (Clostridium) difficile is an opportunistic pathogen known for its ability to colonize the human gut under conditions of dysbiosis. Several aspects of its carbon and amino acid metabolism have been investigated, but its cobamide (vitamin B₁₂ and related cofactors) metabolism remains largely unexplored. C. difficile has seven predicted cobamide-dependent pathways encoded in its genome in addition to a nearly complete cobamide biosynthesis pathway and a cobamide uptake system. To address the importance of cobamides to C. difficile, we studied C. difficile 630 Δerm and mutant derivatives under cobamide-dependent conditions in vitro Our results show that C. difficile can use a surprisingly diverse array of cobamides for methionine and deoxyribonucleotide synthesis and can use alternative metabolites or enzymes, respectively, to bypass these cobamide-dependent processes. C. difficile 630 Δerm produces the cobamide pseudocobalamin when provided the early precursor 5-aminolevulinic acid or the late intermediate cobinamide (Cbi) and produces other cobamides if provided an alternative lower ligand. The ability of C. difficile 630 Δerm to take up cobamides and Cbi at micromolar or lower concentrations requires the transporter BtuFCD. Genomic analysis revealed genetic variations in the btuFCD loci of different C. difficile strains, which may result in differences in the ability to take up cobamides and Cbi. These results together demonstrate that, like other aspects of its physiology, cobamide metabolism in C. difficile is versatile.IMPORTANCE The ability of the opportunistic pathogen Clostridioides difficile to cause disease is closely linked to its propensity to adapt to conditions created by dysbiosis of the human gut microbiota. The cobamide (vitamin B₁₂) metabolism of C. difficile has been underexplored, although it has seven metabolic pathways that are predicted to require cobamide-dependent enzymes. Here, we show that C. difficile cobamide metabolism is versatile, as it can use a surprisingly wide variety of cobamides and has alternative functions that can bypass some of its cobamide requirements. Furthermore, C. difficile does not synthesize cobamides de novo but produces them when given cobamide precursors. A better understanding of C. difficile cobamide metabolism may lead to new strategies to treat and prevent C. difficile-associated disease.

Classification of Riboswitch Families Using Block Location-Based Feature Extraction (BLBFE) Method

Purpose: Riboswitches are special non-coding sequences usually located in mRNAs' un-translated regions and regulate gene expression and consequently cellular function. Furthermore, their interaction with antibiotics has been recently implicated. This raises more interest in development of bioinformatics tools for riboswitch studies. Herein, we describe the development and employment of novel block location-based feature extraction (BLBFE) method for classification of riboswitches. Methods: We have already developed and reported a sequential block finding (SBF) algorithm which, without operating alignment methods, identifies family specific sequential blocks for riboswitch families. Herein, we employed this algorithm for 7 riboswitch families including lysine, cobalamin, glycine, SAM-alpha, SAM-IV, cyclic-di-GMP-I and SAH. Then the study was extended toward implementation of BLBFE method for feature extraction. The outcome features were applied in various classifiers including linear discriminant analysis (LDA), probabilistic neural network (PNN), decision tree and k-nearest neighbors (KNN) classifiers for classification of the riboswitch families. The performance of the classifiers was investigated according to performance measures such as correct classification rate (CCR), accuracy, sensitivity, specificity and f-score. Results: As a result, average CCR for classification of riboswitches was 87.87%. Furthermore, application of BLBFE method in 4 classifiers displayed average accuracies of 93.98% to 96.1%, average sensitivities of 76.76% to 83.61%, average specificities of 96.53% to 97.69% and average f-scores of 74.9% to 81.91%. Conclusion: Our results approved that the proposed method of feature extraction; i.e. BLBFE method; can be successfully used for classification and discrimination of the riboswitch families with high CCR, accuracy, sensitivity, specificity and f-score values.

SAM-VI riboswitch structure and signature for ligand discrimination

Riboswitches are metabolite-sensing, conserved domains located in non-coding regions of mRNA that are central to regulation of gene expression. Here we report the first three-dimensional structure of the recently discovered S-adenosyl-L-methionine responsive SAM-VI riboswitch. SAM-VI adopts a unique fold and ligand pocket that are distinct from all other known SAM riboswitch classes. The ligand binds to the junctional region with its adenine tightly intercalated and Hoogsteen base-paired. Furthermore, we reveal the ligand discrimination mode of SAM-VI by additional X-ray structures of this riboswitch bound to S-adenosyl-L-homocysteine and a synthetic ligand mimic, in combination with isothermal titration calorimetry and fluorescence spectroscopy to explore binding thermodynamics and kinetics. The structure is further evaluated by analysis of ligand binding to SAM-VI mutants. It thus provides a thorough basis for developing synthetic SAM cofactors for applications in chemical and synthetic RNA biology.

Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD. RNA (NEW YORK, N.Y.) 2019;25:1616-1627. [PMID: 31467147 PMCID: PMC6859854 DOI: 10.1261/rna.072538.119]

The nadA motif is a riboswitch candidate present in various Acidobacteria species that was previously identified by bioinformatic analysis of bacterial DNA data sets. More than 100 unique representatives have been identified exclusively upstream of nadA genes, which code for an enzyme in the biosynthetic pathway of the ubiquitous coenzyme NAD⁺ The architecture of nadA motif RNAs suggests they use structurally similar tandem ligand-binding aptamer domains to control translation initiation. Biochemical analyses reveal that the first domain selectively binds ligands carrying an adenosine 5'-diphosphate (5' ADP) moiety, including NAD⁺ and its reduced form, NADH. Genetic analyses indicate that a tandem nadA motif RNA suppresses gene expression when NAD⁺ is abundant, and that both aptamer domains are required for maximal gene regulation. However, we have not observed selective binding of the nicotinamide moiety of NAD⁺ or binding by the second putative aptamer in vitro, despite sequence and structural similarities between the tandem domains.

On the role of mRNA secondary structure in bacterial translation

Messenger RNA (mRNA) is no longer considered as a mere informational molecule whose sole function is to convey the genetic information specified by DNA to the ribosome. Beyond this primary function, mRNA also contains additional instructions that influence the way and the extent to which this message is translated by the ribosome into protein(s). Indeed, owing to its intrinsic propensity to quickly and dynamically fold and form higher order structures, mRNA exhibits a second layer of structural information specified by the sequence itself. Besides influencing transcription and mRNA stability, this additional information also affects translation, and more precisely the frequency of translation initiation, the choice of open reading frame by recoding, the elongation speed, and the folding of the nascent protein. Many studies in bacteria have shown that mRNA secondary structure participates to the rapid adaptation of these versatile organisms to changing environmental conditions by efficiently tuning translation in response to diverse signals, such as the presence of ligands, regulatory proteins, or small RNAs. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Translation Regulation.

Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch

Investigations of most riboswitches remain confined to the ligand-binding aptamer domain. However, during the riboswitch mediated transcription regulation process, the aptamer domain and the expression platform compete for a shared strand. If the expression platform dominates, an anti-terminator helix is formed, and the transcription process is active (ON state). When the aptamer dominates, transcription is terminated (OFF state). Here, we use an expression platform switching experimental assay and structure-based electrostatic simulations to investigate this ON-OFF transition of the full length SAM-I riboswitch and its magnesium concentration dependence. Interestingly, we find the ratio of the OFF population to the ON population to vary non-monotonically as magnesium concentration increases. Upon addition of magnesium, the aptamer domain pre-organizes, populating the OFF state, but only up to an intermediate magnesium concentration level. Higher magnesium concentration preferentially stabilizes the anti-terminator helix, populating the ON state, relatively destabilizing the OFF state. Magnesium mediated aptamer-expression platform domain closure explains this relative destabilization of the OFF state at higher magnesium concentration. Our study reveals the functional potential of magnesium in controlling transcription of its downstream genes and underscores the importance of a narrow concentration regime near the physiological magnesium concentration ranges, striking a balance between the OFF and ON states in bacterial gene regulation.

Analysis and characterization of coenzyme B12 biosynthetic gene clusters and improvement of B12 biosynthesis in Pseudomonas denitrificans ATCC 13867

Coenzyme B12 is an essential cofactor for many enzymes such as glycerol dehydratase, methionine synthase and methylmalonyl-CoA mutase. Herein, we revisited the B12 biosynthetic gene clusters (I and II) in Pseudomonas denitrificans, a well-known industrial producer of the coenzyme B12, to understand the regulation of gene expression and improve the production of coenzyme B12. There were eight operons, seven in cluster I and one in cluster II, and four operons were regulated by B12-responsive riboswitches with a switch-off concentration at ∼5 nM coenzyme B12. DNA sequences of the four riboswitches were partially removed, individually or in combination, to destroy the structures of riboswitches, but no improvement was observed. However, when the whole length of riboswitches in cluster I were completely removed and promoters regulated by the riboswitches were replaced with strong constitutive ones, B12 biosynthesis was improved by up to 2-fold. Interestingly, modification of the promoter region for cluster II, where many (>10) late genes of B12 biosynthesis belong, always resulted in a significant, greater than 6-fold reduction in B12 biosynthesis.

Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans

OLE RNAs represent an unusual class of bacterial noncoding RNAs common in Gram-positive anaerobes. The OLE RNA of the alkaliphile Bacillus halodurans is highly expressed and naturally interacts with at least two RNA-binding proteins called OapA and OapB. The phenotypes of the corresponding knockouts include growth inhibition when exposed to ethanol or other short-chain alcohols or when incubated at modestly reduced temperatures (e.g. 20°C). Intriguingly, the OapA 'PM1' mutant, which carries two amino acid changes to a highly conserved region, yields a dominant-negative phenotype that causes more severe growth defects under these same stress conditions. Herein, we report that the PM1 strain also exhibits extreme sensitivity to elevated Mg²⁺ concentrations, beginning as low as 2 mM. Suppressor mutants predominantly map to genes for aconitate hydratase and isocitrate dehydrogenase, which are expected to alter cellular citrate concentrations. Citrate reduces the severity of the Mg²⁺ toxicity phenotype, but neither the genomic mutations nor the addition of citrate to the medium overcomes ethanol toxicity or temperature sensitivity. These findings reveal that OLE RNA and its protein partners are involved in biochemical responses under several stress conditions, wherein the unusual sensitivity to Mg²⁺ can be independently suppressed by specific genomic mutations.

Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides

A synthetic riboswitch N1, inserted into the 5'-untranslated mRNA region of yeast, regulates gene expression upon binding ribostamycin and neomycin. Interestingly, a similar aminoglycoside, paromomycin, differing from neomycin by only one substituent (amino versus hydroxyl), also binds to the N1 riboswitch, but without affecting gene expression, despite NMR evidence that the N1 riboswitch binds all aminoglycosides in a similar way. Here, to explore the details of structural dynamics of the aminoglycoside-N1 riboswitch complexes, we applied all-atom molecular dynamics (MD) and temperature replica-exchange MD simulations in explicit solvent. Indeed, we found that ribostamycin and neomycin affect riboswitch dynamics similarly but paromomycin allows for more flexibility because its complex lacks the contact between the distinctive 6' hydroxyl group and the G9 phosphate. Instead, a transient hydrogen bond of 6'-OH with A17 is formed, which partially diminishes interactions between the bulge and apical loop of the riboswitch, likely contributing to riboswitch inactivity. In many ways, the paromomycin complex mimics the conformations, interactions, and Na+ distribution of the free riboswitch. The MD-derived interaction network helps understand why riboswitch activity depends on aminoglycoside type, whereas for another aminoglycoside-binding site, aminoacyl-tRNA site in 16S rRNA, activity is not discriminatory.

Conformational switch in the ribosomal protein S1 guides unfolding of structured RNAs for translation initiation

Initiation of bacterial translation requires that the ribosome-binding site in mRNAs adopts single-stranded conformations. In Gram-negative bacteria the ribosomal protein S1 (rS1) is a key player in resolving of structured elements in mRNAs. However, the exact mechanism of how rS1 unfolds persistent secondary structures in the translation initiation region (TIR) is still unknown. Here, we show by NMR spectroscopy that Vibrio vulnificus rS1 displays a unique architecture of its mRNA-binding domains, where domains D3 and D4 provide the mRNA-binding platform and cover the nucleotide binding length of the full-length rS1. D5 significantly increases rS1’s chaperone activity, although it displays structural heterogeneity both in isolation and in presence of the other domains, albeit to varying degrees. The heterogeneity is induced by the switch between the two equilibrium conformations and is triggered by an order-to-order transition of two mutually exclusive secondary structures (β-strand-to-α-helix) of the ‘AERERI’ sequence. The conformational switching is exploited for melting of structured 5′-UTR’s, as the conformational heterogeneity of D5 can compensate the entropic penalty of complex formation. Our data thus provides a detailed understanding of the intricate coupling of protein and RNA folding dynamics enabling translation initiation of structured mRNAs.

Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy

Labeling of long RNA molecules in a site-specific yet generally applicable manner is integral to many spectroscopic applications. Here we present a novel covalent labeling approach that is site-specific and scalable to long intricately folded RNAs. In this approach, a custom-designed DNA strand that hybridizes to the RNA guides a reactive group to target a preselected adenine residue. The functionalized nucleotide along with the concomitantly oxidized 3'-terminus can subsequently be conjugated to two different fluorophores via bio-orthogonal chemistry. We validate this modular labeling platform using a regulatory RNA of 275 nucleotides, the btuB riboswitch of Escherichia coli, demonstrate its general applicability by modifying a base within a duplex, and show its site-selectivity in targeting a pair of adjacent adenines. Native folding and function of the RNA is confirmed on the single-molecule level by using FRET as a sensor to visualize and characterize the conformational equilibrium of the riboswitch upon binding of its cofactor adenosylcobalamin. The presented labeling strategy overcomes size and site constraints that have hampered routine production of labeled RNA that are beyond 200 nt in length.

Riboswitches in Archaea

Background:

Riboswitches are cis-acting, non-coding RNA elements found in the 5’UTR of bacterial mRNA and 3’ UTR of eukaryotic mRNA, that fold in a complex manner to act as receptors for specific metabolites hence altering their conformation in response to the change in concentrations of a ligand or metabolite. Riboswitches function as gene regulators in numerous bacteria, archaea, fungi, algae and plants.

Aim and Objective:

This study identifies different classes of riboswitches in the Archaeal domain of life. Previous studies have suggested that riboswitches carry a conserved aptameric domain in different domains of life. Since Archaea are considered to be the most idiosyncratic organisms it was interesting to look for the conservation pattern of riboswitches in these obviously strange microorganisms.

Materials and Methods:

Completely sequenced Archaeal Genomes present in the NCBI repository were used for studying riboswitches and other ncRNAs. The sequence files in FASTA format were downloaded from NCBI Genome database and information related to these genomes was retrieved from GenBank. Three bioinformatics approaches were used namely, ab initio, consensus structure prediction and statistical model-based prediction for identifying riboswitches.

Results:

Archaeal genomes have a sporadic distribution of putative riboswitches like the TPP, FMN, Guanidine, Lysine and c-di-AMP riboswitches, which are known to occur in bacteria. Also, a class of riboswitch sensing c-di-GMP, a second messenger, has been identified in a few Archaeal organisms.

Conclusion:

This study clearly reveals that bioinformatics methods are likely to play a major role in identifying conserved riboswitches and in establishing how widespread these classes are in all domains of life, even though the final confirmation may come from wet lab methods.

Riboswitch distribution, structure, and function in bacteria

Riboswitches are gene control elements that directly bind to specific ligands to regulate gene expression without the need for proteins. They are found in all three domains of life, including Bacteria, Archaea, and Eukaryota. Riboswitches are mostly spread in bacteria and archaea. In this paper, we discuss the general distribution, structure, and function of 28 different riboswitch classes as we focus our attention on riboswitches in bacteria. Bacterial riboswitches regulate gene expression by four distinct mechanisms. They regulate the expression of a limited number of genes. However, most of these genes are responsible for the synthesis of essential metabolites without which the cell cannot function. Therefore, riboswitch distribution is also important for antibacterial drug development.

"Second-generation" fluorogenic RNA-based sensors

A fluorogenic aptamer can specifically interact with a fluorophore to activate its fluorescence. These nucleic acid-based fluorogenic modules have been dramatically developed over the past decade, and have been used as versatile reporters in the sensor development and for intracellular imaging. In this review, we summarize the design principles, applications, and challenges of the first-generation fluorogenic RNA-based sensors. Moreover, we discuss some strategies to develop next-generation biosensors with improved sensitivity, selectivity, quantification property, and eukaryotic robustness. Using genetically encoded catalytic hairpin assembly strategy as an example, we further introduce a standard protocol to design, characterize, and apply these fluorogenic RNA-based sensors for in vitro detection and cellular imaging of target biomolecules. By incorporating natural RNA machineries, nucleic acid nanotechnology, and systematic evolution approaches, next-generation fluorogenic RNA-based devices can be potentially engineered to be widely applied in cell biology and biomedicine.

A review on native and denaturing purification methods for non-coding RNA (ncRNA)

Recently, non-coding RNA (ncRNA) became the centerpiece of human genome research. Modern ncRNA-based research has revolutionized disease diagnosis and therapeutics. However, decoding structural/functional information of ncRNA requires large amount of pure RNA, and hence effective RNA preparation and purification protocols. This review focuses on purification schemes of synthetic oligonucleotides, particularly liquid chromatographic (LC) techniques as improved alternatives to urea-polyacrylamide gel electrophoresis (urea-PAGE) purification. Moreover, the review summarizes the shortcomings of urea-PAGE purification method and details the chromatographic purification such as affinity, ion-exchange (IE) or size-exclusion (SE) chromatography. Specifically, we discuss denaturing and native RNA purification schemes with newest developments. In short, the review evaluates nucleic acid purification schemes required for various structural analyses.