An RNA sensor for intracellular Mg(2+)

Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome

A crucial step in translation is the translocation of tRNAs through the ribosome. In the transition from one canonical site to the other, the tRNAs acquire intermediate configurations, so-called hybrid states. At this stage, the small subunit is rotated with respect to the large subunit, and the anticodon stem loops reside in the A and P sites of the small subunit, while the acceptor ends interact with the P and E sites of the large subunit. In this work, by means of cryo-EM and particle classification procedures, we visualize the hybrid state of both A/P and P/E tRNAs in an authentic factor-free ribosome complex during translocation. In addition, we show how the repositioning of the tRNAs goes hand in hand with the change in the interplay between S13, L1 stalk, L5, H68, H69, and H38 that is caused by the ratcheting of the small subunit.

A rough guide to the non-coding RNA world of Salmonella

Salmonella species are enterobacterial pathogens that have been exceptionally well investigated with respect to virulence mechanisms, microbial pathogenesis, genome evolution and many fundamental pathways of gene expression and metabolism. While these studies have traditionally focused on protein functions, Salmonella has also become a model organism for RNA-mediated regulation. The present review is dedicated to the non-coding RNA world of Salmonella: it covers small RNAs (sRNAs) that act as post-transcriptional regulators of gene expression, novel Salmonella cis-regulatory RNA elements that sense metabolite and metal ion concentrations (or temperature), and globally acting RNA-binding proteins such as CsrA or Hfq (inactivation of which cause drastic phenotypes and virulence defects). Owing to mosaic genome structure, some of the Salmonella sRNAs are widely conserved in bacteria whereas others are very specific to Salmonella species. Intriguingly, sRNAs of either type (CsrB/C, InvR, SgrS) facilitate cross-talk between the Salmonella core genome and its laterally acquired virulence regions. Work in Salmonella also identified physiological functions (and mechanisms thereof) of RNA that had remained unknown in Escherichia coli, and pioneered the use of high-throughput sequencing technology to identify the sRNA and mRNA targets of bacterial RNA-binding proteins.

Switching the light on plant riboswitches

Riboswitches are natural RNA sensors that affect post-transcriptional processes via their capacity to bind small molecules. To date, these mRNA structures have been shown to regulate the biosynthesis of essential metabolites, including vitamins and amino acids. Although bacterial riboswitches are widespread and characterized, only a single eukaryotic, thiamin-pyrophosphate-binding riboswitch has recently been discovered to direct gene expression by regulating mRNA splicing in fungi, green algae and land plants. It is unclear how widespread riboswitches are and what additional roles they have in eukaryotes. When engineered in plants, riboswitches can function autonomously to modulate gene expression. These discoveries not only trigger novel findings regarding RNA switches in plants, but also spur the exploitation of riboswitches for monitoring metabolite concentrations in planta.

Riboswitches: emerging themes in RNA structure and function

Riboswitches are RNAs capable of binding cellular metabolites using a diverse array of secondary and tertiary structures to modulate gene expression. The recent determination of the three-dimensional structures of parts of six different riboswitches illuminates common features that allow riboswitches to be grouped into one of two types. Type I riboswitches, as exemplified by the purine riboswitch, are characterized by a single, localized binding pocket supported by a largely pre-established global fold. This arrangement limits ligand-induced conformational changes in the RNA to a small region. In contrast, Type II riboswitches, such as the thiamine pyrophosphate riboswitch, contain binding pockets split into at least two spatially distinct sites. As a result, binding induces both local changes to the binding pocket and global architecture. Similar organizational themes are found in other noncoding RNAs, making it possible to begin to build a hierarchical classification of RNA structure based on the spatial organization of their active sites and associated secondary structural elements.

mgtA Expression is induced by rob overexpression and mediates a Salmonella enterica resistance phenotype

Rob is a member of the Sox/Mar subfamily of AraC/XylS-type transcriptional regulators implicated in bacterial multidrug, heavy metal, superoxide, and organic solvent resistance phenotypes. We demonstrate that, in Salmonella enterica, Rob overexpression upregulates the transcription of mgtA, which codes for the MgtA Mg2+ transporter. mgtA was previously characterized as a member of the Mg2+-modulated PhoPQ regulon. Here we demonstrate that Rob (but not its paralog protein SoxS or MarA) is able to induce mgtA transcription in a PhoP-independent fashion by binding to a conserved Mar/Sox/Rob motif localized downstream of the PhoP-box and overlapping the PhoP-dependent transcriptional start site. We found that Rob-induced mgtA expression confers low-level cyclohexane resistance on Salmonella. Because mgtA intactness is required for Rob-induced cyclohexane resistance, provided the AcrAB multidrug efflux pump can be expressed, we postulate that MgtA is involved in the AcrAB-mediated cyclohexane detoxification mechanism promoted by Rob in Salmonella.

RNA switches regulate initiation of translation in bacteria

A large variety of RNA-based mechanisms have been uncovered in all living organisms to regulate gene expression in response to internal and external changes, and to rapidly adapt cell growth in response to these signals. In bacteria, structural elements in the 5′ leader regions of mRNAs have direct effects on translation initiation of the downstream coding sequences. The docking and unfolding of these mRNAs on the 30S subunit are critical steps in the initiation process directly modulating and timing translation. Structural elements can also undergo conformational changes in response to environmental cues (i.e., temperature sensors) or upon binding of a variety oftrans-acting factors, such as metabolites, non-coding RNAs or regulatory proteins. These RNA switches can temporally regulate translation, leading either to repression or to activation of protein synthesis.

Conditional knockdown of hMRS2 results in loss of mitochondrial Mg(2+) uptake and cell death

The human gene MRS2L encodes a mitochondrial protein distantly related to CorA Mg²⁺ transport proteins. Constitutive shRNA-mediated knockdown of hMRS2 in human HEK-293 cell line was found here to cause death. To further study its role in Mg²⁺ transport, we have established stable cell lines with conditionally expressing shRNAs directed against hMRS2L. The cells expressing shRNA for several generations exhibited lower steady-state levels of free mitochondrial Mg²⁺ ([Mg²⁺]_m) and reduced capacity of mitochondrial Mg²⁺ uptake than control cells. Long-term expression of shRNAs resulted in loss of mitochondrial respiratory complex I, decreased mitochondrial membrane potential and cell death. We conclude that hMrs2 is the major transport protein for Mg ⁺ uptake into mitochondria and that expression of hMrs2 is essential for the maintenance of respiratory complex I and cell viability.

Differential regulation by magnesium of the two MsbB paralogs of Shigella flexneri

Shigella flexneri, a gram-negative enteric pathogen, is unusual in that it contains two nonredundant paralogous genes that encode the myristoyl transferase MsbB (LpxM) that catalyzes the final step in the synthesis of the lipid A moiety of lipopolysaccharide. MsbB1 is encoded on the chromosome, and MsbB2 is encoded on the large virulence plasmid present in all pathogenic shigellae. We demonstrate that myristoyl transferase activity due to MsbB2 is detected in limited magnesium medium, but not in replete magnesium medium, whereas that due to MsbB1 is detected under both conditions. MsbB2 increases overall hexa-acylation of lipid A under limited magnesium conditions. Regulation of MsbB2 by magnesium occurs at the level of transcription and is dependent on the conserved magnesium-inducible PhoPQ two-component regulatory pathway. Direct hexanucleotide repeats within the promoter upstream of msbB2 were identified as a putative PhoP binding site, and mutations within the repeats led to diminished PhoP-dependent expression of a transcriptional fusion of lacZ to this promoter. Thus, the virulence plasmid-encoded paralog of msbB is induced under limited magnesium in a PhoPQ-dependent manner. PhoPQ regulates the response of many Enterobacteriaceae to environmental signals, which include modifications of lipid A that confer increased resistance of the organism to stressful environments and antimicrobial peptides. The findings reported here are the first example of gene duplication in which one paralog has selectively acquired the mechanism for differential regulation by PhoPQ. Our findings provide molecular insight into the mechanisms by which each of the two MsbB proteins of S. flexneri likely contributes to pathogenesis.

Mechanism of mRNA destabilization by the glmS ribozyme

An array of highly structured domains that function as metabolite-responsive genetic switches has been found to reside within noncoding regions of certain bacterial mRNAs. In response to intracellular fluctuations of their target metabolite ligands, these RNA elements exert control over transcription termination or translation initiation. However, for a particular RNA class within the 5' untranslated region (UTR) of the glmS gene, binding of glucosamine-6-phosphate stimulates autocatalytic site-specific cleavage near the 5' of the transcript in vitro, resulting in products with 2'-3' cyclic phosphate and 5' hydroxyl termini. The sequence corresponding to this unique natural ribozyme has been subjected to biochemical and structural scrutiny; however, the mechanism by which self-cleavage imparts control over gene expression has yet to be examined. We demonstrate herein that metabolite-induced self-cleavage specifically targets the downstream transcript for intracellular degradation. This degradation pathway relies on action of RNase J1, a widespread ribonuclease that has been proposed to be a functional homolog to the well-studied Escherichia coli RNase E protein. Whereas RNase E only poorly degrades RNA transcripts containing a 5' hydroxyl group, RNase J1 specifically degrades such transcripts in vivo. These findings elucidate key features of the mechanism for genetic control by a natural ribozyme and suggest that there may be fundamental biochemical differences in RNA degradation machinery between E. coli and other bacteria.

Structural basis for recognition of Co2+ by RNA aptamers

Co(2+) binding RNA aptamers were chosen as research models to reveal the structural basis underlying the recognition of Co(2+) by RNA, with the application of two distinct methods. Using the nucleotide analog interference mapping assay, we found strong interference effects after incorporation of the 7-deaza guanosine phosphorotioate analog into the RNA chain at equivalent positions G27 and G28 in aptamer no. 18 and G25 and G26 in aptamer no. 20. The results obtained by nucleotide analog interference mapping suggest that these guanine bases are crucial for the creation of Co(2+) binding sites and that they appear to be involved in the coordination of the ion to the exposed N7 atom of the tandem guanines. Additionally, most 7-deaza guanosine phosphorotioate and 7-deaza adenosine phosphorotioate interferences were located in the common motifs: loop E-like in aptamer no. 18 and kissing dimer in aptamer no. 20. We also found that purine-rich stretches containing guanines with the highest interference values were the targets for hybridization of 6-mers, which are members of the semi-random oligodeoxyribonucleotide library in both aptamers. It transpired that DNA oligomer directed RNase H digestions are sensitive to Co(2+) and, at an elevated metal ion concentration, the hybridization of oligomers to aptamer targets is inhibited, probably due to higher stability and complexity of the RNA structure.

Towards deciphering the principles underlying an mRNA recognition code

Messenger RNAs interact with a number of different molecules that determine the fate of each transcript and contribute to the overall pattern of gene expression. These interactions are governed by specific mRNA signals, which in principle could represent a special mRNA recognition 'code'. Both, small molecules and proteins demonstrate a diversity of mRNA binding modes often dependent on the structural context of the regions surrounding specific target sequences. In this review, we have highlighted recent structural studies that illustrate the diversity of recognition principles used by mRNA binders for timely and specific targeting and processing of the message.

Regulation of magnesium homeostasis in Salmonella: Mg(2+) targets the mgtA transcript for degradation by RNase E

Extracellular Mg(2+) controls the activation of the Salmonella PhoP/PhoQ regulatory system. One of the adaptive responses driven by PhoP/PhoQ includes the transcriptional induction of mgtA and mgtCB, which encode two P-type Mg(2+) transporters. Mg(2+) also controls mgtA expression by a riboswitch located in its 5'-untranslated region (5'UTR). In this work, it was shown that the 5'UTR of both mgtA and mgtCB is responsible for a fine-tuned Mg(2+)-dependent regulation of these genes. Evidence was also provided that the Mg(2+) riboswitch targets the mgtA transcript for degradation by RNase E when cells are grown in high Mg(2+) environments.

Chemical basis of glycine riboswitch cooperativity

The glycine binding riboswitch forms a unique tandem aptamer structure that binds glycine cooperatively. We employed nucleotide analog interference mapping (NAIM) and mutagenesis to explore the chemical basis of glycine riboswitch cooperativity. Based on the interference pattern, at least two sites appear to facilitate cooperative tertiary interactions, namely, the minor groove of the P1 helix from aptamer 1 and the major groove of the P3a helix from both aptamers. Mutation of these residues altered both the cooperativity and binding affinity of the riboswitch. The data support a model in which the P1 helix of the first aptamer participates in a tertiary interaction important for cooperativity, while nucleotides in the P1 helix of the second aptamer interface with the expression platform. These data have direct analogy to well-characterized mutations in hemoglobin, which provides a framework for considering cooperativity in this RNA-based system.

Measuring metals with RNA

In a recent issue of Cell, Winkler and coworkers (Dann et al., 2007) describe in atomic detail the structural changes that allow a specific RNA aptamer (the M box) to regulate transcription in response to changing cellular magnesium levels.

Searching genomes for ribozymes and riboswitches

A discussion of experimental approaches and theoretical difficulties in the identification of ribozymes with novel catalytic functions.

New regulatory RNAs with complex structures have recently been discovered, among them the first catalytic riboswitch, a gene-regulatory RNA sequence with catalytic activity. Here we discuss some of the experimental approaches and theoretical difficulties attached to the identification of new ribozymes in genomes.

Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs

The most widespread riboswitch class, found in organisms from all three domains of life, is responsive to the vitamin B(1) derivative thiamin pyrophosphate (TPP). We have established that a TPP-sensing riboswitch is present in the 3' untranslated region (UTR) of the thiamin biosynthetic gene THIC of all plant species examined. The THIC TPP riboswitch controls the formation of transcripts with alternative 3' UTR lengths, which affect mRNA accumulation and protein production. We demonstrate that riboswitch-mediated regulation of alternative 3' end processing is critical for TPP-dependent feedback control of THIC expression. Our data reveal a mechanism whereby metabolite-dependent alteration of RNA folding controls splicing and alternative 3' end processing of mRNAs. These findings highlight the importance of metabolite sensing by riboswitches in plants and further reveal the significance of alternative 3' end processing as a mechanism of gene control in eukaryotes.

Mutational analysis of the purine riboswitch aptamer domain

The purine riboswitch is one of a number of mRNA elements commonly found in the 5'-untranslated region capable of controlling expression in a cis-fashion via its ability to directly bind small-molecule metabolites. Extensive biochemical and structural analysis of the nucleobase-binding domain of the riboswitch, referred to as the aptamer domain, has revealed that the mRNA recognizes its cognate ligand using an intricately folded three-way junction motif that completely encapsulates the ligand. High-affinity binding of the purine nucleobase is facilitated by a distal loop-loop interaction that is conserved between both the adenine and guanine riboswitches. To understand the contribution of conserved nucleotides in both the three-way junction and the loop-loop interaction of this RNA, we performed a detailed mutagenic survey of these elements in the context of an adenine-responsive variant of the xpt-pbuX guanine riboswitch from Bacillus subtilis. The varying ability of these mutants to bind ligand as measured by isothermal titration calorimetry uncovered the conserved nucleotides whose identity is required for purine binding. Crystallographic analysis of the bound form of five mutants and chemical probing of their free state demonstrate that the identity of several universally conserved nucleotides is not essential for formation of the RNA-ligand complex but rather for maintaining a binding-competent form of the free RNA. These data show that conservation patterns in riboswitches arise from a combination of formation of the ligand-bound complex, promoting an open form of the free RNA, and participating in the secondary structural switch with the expression platform.

Metal sensing by RNA in bacteria: exception or rule?

Until 2006, it was believed that bacteria control their intracellular metal ion concentrations exclusively through metal-sensing proteins. However, the detection of the first riboswitch that uses a small ion, Mg2+, as ligand to regulate gene expression in Salmonella challenged this assumption. Now, the discovery and in-depth characterization of a second metal-ion-sensing riboswitch that seems to be ubiquitously present in Gram-positive bacteria suggest that metal sensing by RNAs may represent a widespread mechanism.

Structure and mechanism of a metal-sensing regulatory RNA

Organisms maintain the correct balance of intracellular metals primarily through metal-sensing proteins that control transport and storage of the target ion(s). Here, we reveal the basis of metal sensing and genetic control by a metalloregulatory RNA. Our data demonstrate that a previously uncharacterized orphan riboswitch, renamed the "M-box," is a divalent metal-sensing RNA involved in Mg(2+) homeostasis. A combination of genetic, biochemical, and biophysical techniques demonstrate that Mg(2+) induces a compacted tertiary architecture for M-box RNAs that regulates the accessibility of nucleotides involved in genetic control. Molecular details are provided by crystallographic structure determination of a Mg(2+)-bound M-box RNA. Given the distribution of this RNA element, it may constitute a common mode for bacterial metal ion regulation, and its discovery suggests the possibility of additional RNA-based metal sensors in modern and primordial organisms.

Stimulus-dependent differential regulation in the Escherichia coli PhoQ PhoP system

In Escherichia coli, Salmonella, and related bacteria, the PhoQ-PhoP system regulates the expression of a large collection of genes in response to conditions of low magnesium or to the presence of certain antimicrobial peptides. We measured transcription of four PhoP-regulated promoters in E. coli that have significantly different PhoP-binding sites. Surprisingly, three promoters show identical responses to magnesium concentrations that range over four orders of magnitude. By analyzing and testing a simple model of transcriptional regulation, we find an explanation for this puzzle and show that these promoters are indeed differentially regulated at sufficiently high levels of stimulus. We then use this analysis to infer an effective level of phosphorylated PhoP as a function of magnesium stimulus. Our results demonstrate that differential regulation generally depends on the strength of the stimulus and highlight how quantitative analysis of stimulus-response curves can be used to infer properties of cell regulatory circuits that cannot be easily obtained from in vitro measurements.

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

Although various functions of RNA are carried out in conjunction with proteins, some catalytic RNAs, or ribozymes, which contribute to a range of cellular processes, require little or no assistance from proteins. Furthermore, the discovery of metabolite-sensing riboswitches and other types of RNA sensors has revealed RNA-based mechanisms that cells use to regulate gene expression in response to internal and external changes. Structural studies have shown how these RNAs can carry out a range of functions. In addition, the contribution of ribozymes and riboswitches to gene expression is being revealed as far more widespread than was previously appreciated. These findings have implications for understanding how cellular functions might have evolved from RNA-based origins.

Structural features of metabolite-sensing riboswitches

Riboswitches, metabolite-sensing RNA elements that are present in untranslated regions of the transcripts that they regulate, possess extensive tertiary structure to couple metabolite binding to genetic control. Here we discuss recently published structures from four riboswitch classes and compare these natural RNA structures to those of in-vitro-selected RNA aptamers, which bind ligands similar to those of the riboswitches. In addition, we examine the glmS riboswitch - the first example of a ribozyme-based riboswitch. This RNA provides the latest twist in the riboswitch field and portends exciting advances in the coming years. Our knowledge of the mechanisms underlying genetic regulation by riboswitches has increased mightily in recent years and will continue to grow as new riboswitch classes and ligands are discovered and structurally characterized.

Ligand recognition determinants of guanine riboswitches

Guanine riboswitches negatively modulate transcription upon guanine binding. The aptamer domain is organized around a three-way junction which forms the ligand binding site. Using currently available 89 guanine aptamer sequences, a consensus secondary structure is deduced and reveals differences from the previously identified aptamer consensus. Three positions are found to display different nucleotide requirements. Using a 2-aminopurine binding assay, we show that variations are allowed depending on the aptamer context. However, changes at position 48 markedly decrease ligand binding in a context-independent fashion. This is consistent with previous observations with the adenine riboswitch in which position 48 was proposed to interact with position 74, which normally base pairs with the ligand. The in vivo transcriptional control of endogenous Bacillus subtilis guanine riboswitches was studied using RT-qPCR assays. The ratio of elongated/terminated transcripts is decreased in presence of a high concentration of guanine but is dependent on the riboswitch analyzed. In general, the aptamer-2AP complex affinity correlates well with the in vivo regulation efficiency of the corresponding riboswitch. These studies suggest that core variations of guanine aptamers are used to produce a spectrum of ligand binding affinities which is used in vivo by host riboswitches to perform gene regulation.

Fluctuations of transfer RNAs between classical and hybrid states

Adjacent transfer RNAs (tRNAs) in the A- and P-sites of the ribosome are in dynamic equilibrium between two different conformations called classical and hybrid states before translocation. Here, we have used single-molecule fluorescence resonance energy transfer to study the effect of Mg(2+) on tRNA dynamics with and without an acetyl group on the A-site tRNA. When the A-site tRNA is not acetylated, tRNA dynamics do not depend on [Mg(2+)], indicating that the relative positions of the substrates for peptide-bond formation are not affected by Mg(2+). In sharp contrast, when the A-site tRNA is acetylated, Mg(2+) lengthens the lifetime of the classical state but does not change the lifetime of the hybrid state. Based on these findings, the classical state resembles a state with direct stabilization of tertiary structure by Mg(2+) ions whereas the hybrid state resembles a state with little Mg(2+)-assisted stabilization. The antibiotic viomycin, a translocation inhibitor, suppresses tRNA dynamics, suggesting that the enhanced fluctuations of tRNAs after peptide-bond formation drive spontaneous attempts at translocation by the ribosome.

A Mg2+-responding RNA that controls the expression of a Mg2+ transporter

Mg2+ is the most abundant divalent cation in biological systems. It is required for ATP-mediated enzymatic reactions and as a stabilizer of ribosomes and membranes. The enteric bacterium Salmonella enterica serovar Typhimurium harbors three Mg2+ transporters and a regulatory system-termed PhoP/PhoQ-whose activity is regulated by the extracytoplasmic levels of Mg2+. We have determined that expression of the PhoP-activated Mg2+ transporter MgtA is also controlled by its 5'-untranslated region (5'UTR). The 5'UTR of the mgtA gene can adopt different stem-loop structures depending on the Mg2+ levels, which determine whether transcription reads through into the mgtA-coding region or stops within the 5'UTR. This makes the mgtA 5'UTR the first example of a cation-responding riboswitch. The initiation of mgtA transcription responds to extracytoplasmic Mg2+, and its elongation into the coding region to cytoplasmic Mg2+, which provides a singular example where the same ligand is sensed in different cellular compartments to regulate disparate steps in gene transcription. The PhoP-activated Mg2+ transporter mgtB is also regulated by Mg2+ in a strain lacking the Mg2+ sensor PhoQ, suggesting the presence of additional Mg2+-responding devices.

The expanding universe of noncoding RNAs

The 71st Cold Spring Harbor Symposium on Quantitative Biology celebrated the numerous and expanding roles of regulatory RNAs in systems ranging from bacteria to mammals. It was clearly evident that noncoding RNAs are undergoing a renaissance, with reports of their involvement in nearly every cellular process. Previously known classes of longer noncoding RNAs were shown to function by every possible means-acting catalytically, sensing physiological states through adoption of complex secondary and tertiary structures, or using their primary sequences for recognition of target sites. The many recently discovered classes of small noncoding RNAs, generally less than 35 nucleotides in length, most often exert their effects by guiding regulatory complexes to targets via base-pairing. With the ability to analyze the RNA products of the genome in ever greater depth, it has become clear that the universe of noncoding RNAs may extend far beyond the boundaries we had previously imagined. Thus, as much as the Symposium highlighted exciting progress in the field, it also revealed how much farther we must go to understand fully the biological impact of noncoding RNAs.

Structural studies of the purine and SAM binding riboswitches

Riboswitches are recently discovered genetic regulatory elements found in the 5'-untranslated regions of bacterial mRNAs that act through their ability to specifically bind small-molecule metabolites. Binding of the ligand to the aptamer domain of the riboswitch is communicated to a second domain, the expression platform, which directs transcription or translation of the mRNA. To understand this process on a molecular level, structures of three of these riboswitches bound to their cognate ligands have been solved by X-ray crystallography: the purine, thiamine pyrophosphate (TPP), and S-adenosylmethionine (SAM-I) binding aptamer domains. These studies have uncovered three common themes between the otherwise different molecules. First, the natural RNA aptamers recognize directly or indirectly almost every feature of their ligand to achieve extraordinary specificity. Second, all of these RNAs use a complex tertiary architecture to establish the binding pocket. Finally, in each case, ligand binding serves to stabilize a helix that communicates the binding event to the expression platform. Here, we discuss these properties of riboswitches in the context of the purine and SAM-I riboswitches.

Riboswitches: small-molecule recognition by gene regulatory RNAs

Riboswitches demonstrate the ability of highly structured RNA molecules to recognize small-molecule metabolites with high specificity and subsequently harness the binding energy for the control of gene expression. Crystal structures have now been determined for the metabolite-binding domains of riboswitches that respond to purines, thiamine pyrophosphate and S-adenosylmethionine, as well as for the glmS ribozyme, a catalytic riboswitch that is activated by the metabolite glucosamine-6-phosphate. In addition to these riboswitch structures, a solution NMR structure has been reported for a ribosensor that regulates heat shock genes in response to changes in temperature. These studies reveal the structural basis of the remarkable selectivity of riboswitches and, in conjunction with biochemical and biophysical measurements, provide a framework for detailed mechanistic understanding of riboswitch-mediated modulation of gene expression.

Small noncoding RNAs controlling pathogenesis

Infectious diseases are a leading cause of mortality worldwide. A major challenge in achieving their eradication is a better understanding of bacterial pathogenesis processes. The recent discovery of small noncoding RNAs (sRNAs) as modulators of gene expression in response to environmental cues has brought a new insight into bacterial regulation. sRNAs coordinate complex networks of stress adaptation and virulence gene expression. sRNAs generally ensure such a regulation by pairing to mRNAs of effector and/or regulatory genes, or by binding to proteins. An updated view on bacterial models responsible for important infections illustrates the key role of sRNAs in the control of pathogenesis.

The intricate world of riboswitches

Riboswitches are segments of the 5'-untranslated region of certain bacterial mRNAs that upon recognition of specific ligands modify the expression of a protein(s) encoded in the message. These proteins are responsible for the biosynthesis or transport of ligands, which are typically organic molecules but could also be metal ions. Riboswitch-mediated control of gene expression might be thermodynamic or kinetic, depending on the rate of transcription elongation by RNA polymerase and the structures adopted by the riboswitch RNA. Certain 5'-untranslated regions harbor two riboswitches in tandem that bind to different ligands. Thus, RNA sensors can respond to metabolic changes by modifying gene expression in ways previously thought to be exclusive of proteins.

The THI-box Riboswitch, or How RNA Binds Thiamin Pyrophosphate

Riboswitches are genetic control elements present mainly in the 5' untranslated regions of messenger RNAs that, upon binding of a small metabolite (like some vitamins, amino acids, and nucleobases), undergo conformational changes, affecting the expression of downstream genes. Structural studies of riboswitches are important for understanding how they recognize their ligands with high specificity and affinity. The thiamin pyrophosphate binding riboswitch (THI- box) is widely distributed in the three kingdoms of life and is involved in very distinct modes of gene regulation. Three recent THI-box structural analyses revealed how polyanionic RNA is able to bind a molecule with a negatively charged pyrophosphate group like thiamin pyrophosphate (TPP) and how it can discriminate between TPP and monophosphorylated analog molecules. These studies give insight into the genetic regulatory mechanisms in which the THI-box is involved.

Core requirements of the adenine riboswitch aptamer for ligand binding

The adenine riboswitch aptamer, the A box, positively regulates gene expression upon adenine binding. To provide insight into structure-function relationships, important for the adenine riboswitch aptamer, we have created alignments for six aptamer sequences that reveal the core requirements. In addition, 2-aminopurine (2AP) binding studies have been used to test the consensus sequence derived from the alignment. Overall, the consensus secondary structure is consistent with 2AP binding studies. However, a position in the core, previously identified as variable, shows restriction in nucleotide sequence. Furthermore, this restriction is found to be related with the ligand specificity of the riboswitch. The implications of this relationship for the riboswitch gene regulation mechanism are discussed.

From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements

Structural elements in the 5' region of a bacterial mRNA can have major effects on expression of downstream coding sequences. Folding of the nascent RNA into the helix of an intrinsic transcriptional terminator results in premature termination of transcription and in failure to synthesize the full-length transcript. Structure in the translation initiation region of an mRNA blocks access of the translation initiation complex to the ribosome binding site, thereby preventing protein synthesis. RNA structures can also affect the stability of an RNA by altering sensitivity to ribonucleases. A wide variety of mechanisms have been uncovered in which changes in mRNA structure in response to a regulatory signal are used to modulate gene expression in bacteria. These systems allow the cell to recognize an impressive array of signals, and to monitor those signals in many different ways.

Metal sensor proteins: nature's metalloregulated allosteric switches

Metalloregulatory proteins control the expression of genes that allow organisms to quickly adapt to chronic toxicity or deprivation of both biologically essential metal ions and heavy metal pollutants found in their microenvironment. Emerging evidence suggests that metal ion homeostasis and resistance defines an important tug-of-war in human host-bacterial pathogen interactions. This adaptive response originates with the formation of "metal receptor" complexes of exquisite selectivity. In this perspective, we summarize consensus structural features of metal sensing coordination complexes and the evolution of distinct metal selectivities within seven characterized metal sensor protein families. In addition, we place recent efforts to understand the structural basis of metal-induced allosteric switching of these metalloregulatory proteins in a thermodynamic framework, and review the degree to which coordination chemistry drives changes in protein structure and dynamics in selected metal sensor systems. New insights into how metal sensor proteins function in the complex intracellular milieu of the cytoplasm of cells will require a more sophisticated understanding of the "metallome" and will benefit greatly from ongoing collaborative efforts in bioinorganic, biophysical and analytical chemistry, structural biology and microbiology.

Identification of separate structural features that affect rate and cation concentration dependence of self-cleavage by the Neurospora VS ribozyme

The cleavage site of the Neurospora VS ribozyme is located in an internal loop in a hairpin called stem-loop I. Stem-loop I undergoes a cation-dependent structural change to adopt a conformation, termed shifted, that is required for activity. Using site-directed mutagenesis and kinetic analyses, we show here that the insertion of a single-stranded linker between stem-loop I and the rest of the ribozyme increases the observed self-cleavage rate constant by 2 orders of magnitude without affecting the Mg(2+) requirement of the reaction. A distinct set of mutations that favors the formation of the shifted conformation of stem-loop I decreases the Mg(2+) requirement by an order of magnitude with little or no effect on the observed cleavage rate under standard reaction conditions. Similar trends were seen in reactions that contained Li(+) instead of Mg(2+). Mutants with lower ionic requirements also exhibited increased thermostability, providing evidence that the shifted conformation of stem-loop I favors the formation of the active conformation of the RNA. In natural, multimeric VS RNA, where a given ribozyme core is flanked by one copy of stem-loop I immediately upstream and another copy 0.7 kb downstream, cleavage at the downstream site is strongly preferred, providing evidence that separation of stem-loop I from the ribozyme core reflects the naturally evolved organization of the RNA.

Utilizing RNA aptamers to probe a physiologically important heme-regulated cellular network

Broadly applicable strategies facilitating direct and selective modulation of the intracellular levels of physiologically important small molecules are essential for dissecting their integral and multiple roles in cellular processes. Therefore, we have been exploring the suitability of RNA aptamers for this purpose. Using the Escherichia coli heme biosynthetic pathway as a simple model of a negative feedback regulated process, we show that heme-binding RNA aptamers, developed in vitro and expressed intracellularly, induce a heme-dependent growth defect in an E. coli heme auxotroph defective in converting delta-aminolevulinic (delta-ALA) acid into downstream products. Relative to a control oligonucleotide, the aptamers also induce delta-ALA accumulation in cells grown under heme-limiting conditions. Increasing the concentration of heme in the media completely reverses both the growth defect and delta-ALA accumulation, except for two aptamers for which reversal is partial. Thus, these aptamers specifically target their cognate ligand in vivo and functionally modulate its intracellular concentration, demonstrating that RNA aptamers are useful tools for elucidating the role of heme and possibly other small molecules in regulating cellular networks.

Bacterial gene regulation: metal ion sensing by proteins or RNA

Until recently, metal sensing in bacteria seemed to be accomplished exclusively by metalloregulatory proteins; however, a surprising new finding is that a metal ion itself can act as a riboswitch ligand to shut down gene expression. Interestingly, this ion is Mg(2+), known to be required for a wide variety of cellular functions and for correct folding of RNAs. It remains to be discovered whether other ion-dependent riboswitches exist, which would open up a new dimension for regulatory RNAs.

A structural basis for Mg2+ homeostasis and the CorA translocation cycle

We describe the CorA Mg(2+) transporter homologue from Thermotoga maritima in complex with 12 divalent cations at 3.7 A resolution. One metal is found near the universally conserved GMN motif, apparently stabilized within the transmembrane region. This portion of the selectivity filter might discriminate between the size and preferred coordination geometry of hydrated substrates. CorA may further achieve specificity by requiring the sequential dehydration of substrates along the length of its approximately 55 A long pore. Ten metal sites identified within the cytoplasmic funnel domain are linked to long extensions of the pore helices and regulate the transport status of CorA. We have characterized this region as an intrinsic divalent cation sensor and provide evidence that it functions as a Mg(2+)-specific homeostatic molecular switch. A proteolytic protection assay, biophysical data, and comparison to a soluble domain structure from Archaeoglobus fulgidus have revealed the potential reaction coordinate for this diverse family of transport proteins.