Monitoring intermediate folding states of the td group I intron in vivo

Advances in RNA 3D Structure Modeling Using Experimental Data

RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA structures using x-ray crystallography is both laborious and demands expertise, thus, hindering our comprehension of RNA structural biology. The computational modeling of RNA structure was a milestone in the birth of bioinformatics. Although computational modeling has been greatly improved over the last decade showing many successful cases, the accuracy of such computational modeling is not only length-dependent but also varies according to the complexity of the structure. To increase credibility, various experimental data were integrated into computational modeling. In this review, we summarize the experiments that can be integrated into RNA structure modeling as well as the computational methods based on these experimental data. We also demonstrate how computational modeling can help the experimental determination of RNA structure. We highlight the recent advances in computational modeling which can offer reliable structure models using high-throughput experimental data.

Accumulation of Stable Full-Length Circular Group I Intron RNAs during Heat-Shock

Group I introns in nuclear ribosomal RNA of eukaryotic microorganisms are processed by splicing or circularization. The latter results in formation of full-length circular introns without ligation of the exons and has been proposed to be active in intron mobility. We applied qRT-PCR to estimate the copy number of circular intron RNA from the myxomycete Didymium iridis. In exponentially growing amoebae, the circular introns are nuclear and found in 70 copies per cell. During heat-shock, the circular form is up-regulated to more than 500 copies per cell. The intron harbours two ribozymes that have the potential to linearize the circle. To understand the structural features that maintain circle integrity, we performed chemical and enzymatic probing of the splicing ribozyme combined with molecular modeling to arrive at models of the inactive circular form and its active linear counterpart. We show that the two forms have the same overall structure but differ in key parts, including the catalytic core element P7 and the junctions at which reactions take place. These differences explain the relative stability of the circular species, demonstrate how it is prone to react with a target molecule for circle integration and thus supports the notion that the circular form is a biologically significant molecule possibly with a role in intron mobility.

Progress and challenges for chemical probing of RNA structure inside living cells

Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell. A full description of its structure is critical to understanding RNA function. Decades of research have focused on utilizing chemical tools to interrogate the structures of RNAs, with recent focus shifting to performing experiments inside living cells. This Review will detail the design and utility of chemical reagents used in RNA structure probing. We also outline how these reagents have been used to gain a deeper understanding of RNA structure in vivo. We review the recent merger of chemical probing with deep sequencing. Finally, we outline some of the hurdles that remain in fully characterizing the structure of RNA inside living cells, and how chemical biology can uniquely tackle such challenges.

Mapping RNA structure in vitro using nucleobase-specific probes

RNAs have to adopt specific three-dimensional structures to fulfill their biological functions. Therefore exploring RNA structure is of interest to understand RNA-dependent processes. Chemical probing in vitro is a very powerful tool to investigate RNA molecules under a variety of conditions. Among the most frequently used chemical reagents are the nucleobase-specific probes dimethyl sulfate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate (CMCT) and β-ethoxy-α-ketobutyraldehyde (kethoxal). These chemical reagents modify nucleotides which are not involved in hydrogen bonding or protected by a ligand, such as proteins or metabolites. Upon performing modification reactions with all three chemicals the accessibility of all four nucleobases can be determined. With this fast and inexpensive method local changes in RNA secondary and tertiary structure, as well as the formation of contacts between RNA and its ligands can be detected independent of the RNA's length.

Chemical probing of RNA in living cells

RNAs need to adopt a specific architecture to exert their task in cells. While significant progress has been made in describing RNA folding landscapes in vitro, understanding intracellular RNA structure formation is still in its infancy. This is in part due to the complex nature of the cellular environment but also to the limited availability of suitable methodologies. To assess the intracellular structure of large RNAs, we recently applied a chemical probing technique and a metal-induced cleavage assay in vivo. These methods are based on the fact that small molecules, like dimethyl sulfate (DMS), or metal ions, such as Pb(2+), penetrate and spread throughout the cell very fast. Hence, these chemicals are able to modify accessible RNA residues or to induce cleavage of the RNA strand in the vicinity of a metal ion in living cells. Mapping of these incidents allows inferring information on the intracellular conformation, metal ion binding sites or ligand-induced structural changes of the respective RNA molecule. Importantly, in vivo chemical probing can be easily adapted to study RNAs in different cell types.

On the importance of cotranscriptional RNA structure formation

The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.

Evaluation of RNA chaperone activity in vivo and in vitro using misfolded group I ribozymes

Here two methods to measure RNA chaperone activity in vivo and in vitro are described. In both assays folding of a misfolded group I intron RNA into the splicing-competent form in the presence of proteins with RNA chaperone activity is measured. Folding is evaluated indirectly by assessing the difference in splicing activity with or without proteins with RNA chaperone activity. In vitro, we use the thymidylate synthase (td) group I intron of phage T4 that is split into two halves. As a consequence this split ribozyme is only capable to fold and in turn to splice in trans at elevated temperatures. Proteins with RNA chaperone activity enable splicing of the split intron at lower temperatures. This difference in splicing activity is measured to assess the efficacy of the RNA chaperone. In vivo, a mutant variant of the td group I intron is trapped in a misfolded conformation, resulting in a reduced splicing activity. Over-expression of proteins with RNA chaperone activity results in an increase in splicing in vivo, as these proteins resolve the misfolded conformation.

Mss116p: a DEAD-box protein facilitates RNA folding

RNA folding is an essential aspect underlying RNA-mediated cellular processes. Many RNAs, including large, multi-domain ribozymes, are capable of folding to the native, functional state without assistance of a protein cofactor in vitro. In the cell, trans-acting factors, such as proteins, are however known to modulate the structure and thus the fate of an RNA. DEAD-box proteins, including Mss116p, were recently found to assist folding of group I and group II introns in vitro and in vivo. The underlying mechanism(s) have been studied extensively to explore the contribution of ATP hydrolysis and duplex unwinding in helicase-stimulated intron splicing. Here we summarize the ongoing efforts to understand the novel role of DEAD-box proteins in RNA folding.

Predicting and modeling RNA architecture

A general approach for modeling the architecture of large and structured RNA molecules is described. The method exploits the modularity and the hierarchical folding of RNA architecture that is viewed as the assembly of preformed double-stranded helices defined by Watson-Crick base pairs and RNA modules maintained by non-Watson-Crick base pairs. Despite the extensive molecular neutrality observed in RNA structures, specificity in RNA folding is achieved through global constraints like lengths of helices, coaxiality of helical stacks, and structures adopted at the junctions of helices. The Assemble integrated suite of computer tools allows for sequence and structure analysis as well as interactive modeling by homology or ab initio assembly with possibilities for fitting within electronic density maps. The local key role of non-Watson-Crick pairs guides RNA architecture formation and offers metrics for assessing the accuracy of three-dimensional models in a more useful way than usual root mean square deviation (RMSD) values.

RNA folding in living cells

RNA folding is the most essential process underlying RNA function. While significant progress has been made in understanding the forces driving RNA folding in vitro, exploring the rules governing intracellular RNA structure formation is still in its infancy. The cellular environment hosts a great diversity of factors that potentially influence RNA folding in vivo. For example, the nature of transcription and translation is known to shape the folding landscape of RNA molecules. Trans-acting factors such as proteins, RNAs and metabolites, among others, are also able to modulate the structure and thus the fate of an RNA. Here we summarize the ongoing efforts to uncover how RNA folds in living cells.

DEAD-box protein facilitated RNA folding in vivo

In yeast mitochondria the DEAD-box helicase Mss116p is essential for respiratory growth by acting as group I and group II intron splicing factor. Here we provide the first structure-based insights into how Mss116p assists RNA folding in vivo. Employing an in vivo chemical probing technique, we mapped the structure of the ai5γ group II intron in different genetic backgrounds to characterize its intracellular fold. While the intron adopts the native conformation in the wt yeast strain, we found that the intron is able to form most of its secondary structure, but lacks its tertiary fold in the absence of Mss116p. This suggests that ai5γ is largely unfolded in the mss116-knockout strain and requires the protein at an early step of folding. Notably, in this unfolded state misfolded substructures have not been observed. As most of the protein-induced conformational changes are located within domain D1, Mss116p appears to facilitate the formation of this largest domain, which is the scaffold for docking of other intron domains. These findings suggest that Mss116p assists the ordered assembly of the ai5γ intron in vivo.

Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron

The td group I intron interrupting the thymidylate synthase (TS) gene of phage T4 is a mobile intron that encodes the homing endonuclease I-TevI. Efficient RNA splicing of the intron is required to restore function of the TS gene, while expression of I-TevI from within the intron is required to initiate intron mobility. Three distinct layers of regulation temporally limit I-TevI expression to late in the T4 infective cycle, yet the biological rationale for stringent regulation has not been tested. Here, we deleted key control elements to deregulate I-TevI expression at early and middle times post T4 infection. Strikingly, we found that deregulation of I-TevI, or of a catalytically inactive variant, generated a thymidine-dependent phenotype that is caused by a reduction in td intron splicing. Prematurely terminating I-TevI translation restores td splicing, full-length TS synthesis, and rescues the thymidine-dependent phenotype. We suggest that stringent translational control of I-TevI evolved to prevent the ribosome from disrupting key structural elements of the td intron that are required for splicing and TS function at early and middle times post T4 infection. Analogous translational regulatory mechanisms in unrelated intron-open reading frame arrangements may also function to limit deleterious consequences on splicing and host gene function.

Protein-facilitated folding of group II intron ribozymes

Multiple studies hypothesize that DEAD-box proteins facilitate folding of the ai5gamma group II intron. However, these conclusions are generally inferred from splicing kinetics, and not from direct monitoring of DEAD-box protein-facilitated folding of the intron. Using native gel electrophoresis and dimethyl sulfate structural probing, we monitored Mss-116-facilitated folding of ai5gamma intron ribozymes and a catalytically active self-splicing RNA containing full-length intron and short exons. We found that the protein directly stimulates folding of these RNAs by accelerating formation of the compact near-native state. This process occurs in an ATP-independent manner, although ATP is required for the protein turnover. As Mss 116 binds RNA nonspecifically, most binding events do not result in the formation of the compact state, and ATP is required for the protein to dissociate from such nonproductive complexes and rebind the unfolded RNA. Results obtained from experiments at different concentrations of magnesium ions suggest that Mss 116 stimulates folding of ai5gamma ribozymes by promoting the formation of unstable folding intermediates, which is then followed by a cascade of folding events resulting in the formation of the compact near-native state. Dimethyl sulfate probing results suggest that the compact state formed in the presence of the protein is identical to the near-native state formed more slowly in its absence. Our results also indicate that Mss 116 does not stabilize the native state of the ribozyme, but that such stabilization results from binding of attached exons.

Exploring RNA structure by integrative molecular modelling

RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded in three dimensions (3D) and used as building blocks assembled manually during a bioinformatic interactive process. Comparing the models to the corresponding crystal structures has validated the method as being powerful to predict the RNA topology and architecture while being less accurate regarding the prediction of base-base interactions. These aspects as well as the necessary steps towards automation will be discussed.

Tertiary architecture of the Oceanobacillus iheyensis group II intron

Group II introns are large ribozymes that act as self-splicing and retrotransposable RNA molecules. They are of great interest because of their potential evolutionary relationship to the eukaryotic spliceosome, their continued influence on the organization of many genomes in bacteria and eukaryotes, and their potential utility as tools for gene therapy and biotechnology. One of the most interesting features of group II introns is their relative lack of nucleobase conservation and covariation, which has long suggested that group II intron structures are stabilized by numerous unusual tertiary interactions and backbone-mediated contacts. Here, we provide a detailed description of the tertiary interaction networks within the Oceanobacillus iheyensis group IIC intron, for which a crystal structure was recently solved to 3.1 A resolution. The structure can be described as a set of several intricately constructed tertiary interaction nodes, each of which contains a core of extended stacking networks and elaborate motifs. Many of these nodes are surrounded by a web of ribose zippers, which appear to further stabilize local structure. As predicted from biochemical and genetic studies, the group II intron provides a wealth of new information on strategies for RNA folding and tertiary structural organization.

Probing RNA structure within living cells

RNA folding is the most fundamental process underlying RNA function. RNA structure and associated folding paradigms have been intensively studied in vitro. However, in vivo RNA structure formation has only been explored to a limited extent. To determine the influence of the cellular environment, which differs significantly from the in vitro refolding conditions, on RNA architecture, we have applied a chemical probing technique to assess the structure of catalytic RNAs in living cells. This method is based on the fact that chemicals like dimethyl sulfate readily penetrate cells and modify specific atoms of RNA bases (N1-A, N3-C), provided that these positions are solvent accessible. By mapping the modified residues, one gains substantial information on the architecture of the target RNA on the secondary and tertiary structure level. This method also allows exploration of interactions of the target RNA with ligands such as proteins, metabolites, or other RNA molecules and associated conformational changes. In brief, in vivo chemical probing is a powerful tool to investigate RNA structure in its natural environment and can be easily adapted to study RNAs in different cell types.

Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

Twin-ribozyme introns contain a branching ribozyme (GIR1) followed by a homing endonuclease (HE) encoding sequence embedded in a peripheral domain of a group I splicing ribozyme (GIR2). GIR1 catalyses the formation of a lariat with 3 nt in the loop, which caps the HE mRNA. GIR1 is structurally related to group I ribozymes raising the question about how two closely related ribozymes can carry out very different reactions. Modelling of GIR1 based on new biochemical and mutational data shows an extended substrate domain containing a GoU pair distinct from the nucleophilic residue that dock onto a catalytic core showing a different topology from that of group I ribozymes. The differences include a core J8/7 region that has been reduced and is complemented by residues from the pre-lariat fold. These findings provide the basis for an evolutionary mechanism that accounts for the change from group I splicing ribozyme to the branching GIR1 architecture. Such an evolutionary mechanism can be applied to other large RNAs such as the ribonuclease P.

Dissecting RNA chaperone activity

Many RNA-binding proteins help RNAs to fold via their RNA chaperone activity. This term has been used widely without accounting for the diversity of the observed reactions, which include complex events like restructuring of misfolded catalytic RNAs, promoting the assembly of RNA-protein complexes, and mediating RNA-RNA interactions. Proteins display very diverse activities depending on the assays used to measure RNA chaperone activity. To classify proteins with this activity, we compared three exemplary proteins from E. coli, host factor Hfq, ribosomal protein S1, and the histone-like protein StpA for their abilities to promote two simple reactions, RNA annealing and strand displacement. The results of a FRET-based assay show that S1 promotes only RNA strand displacement while Hfq solely enhances RNA annealing. StpA, in contrast, is active in both reactions. To test whether the two activities can be assigned to different domains of the bipartite-structured StpA, we assayed the purified N- and C- terminal domains separately. While both domains are unable to promote RNA annealing, we can attribute the RNA strand displacement activity of StpA to the C-terminal domain. Correlating with their RNA annealing activities, only Hfq and full-length StpA display simultaneous binding of two RNAs, suggesting a matchmaker-like model for this activity. For StpA, this "RNA crowding" requires protein-protein interactions, since a dimerization-deficient StpA mutant lost the ability to bind and anneal two RNAs. These results underline the difference between the two reaction types, making it necessary to distinguish and classify proteins according to their specific RNA chaperone activities.

Group II intron folding under near-physiological conditions: collapsing to the near-native state

The folding of group II intron ribozymes has been studied extensively under optimal conditions for self-splicing in vitro (42 degrees C and high magnesium ion concentrations). In these cases, the ribozymes fold directly to the native state by an apparent two-state mechanism involving the formation of an obligate intermediate within intron domain 1. We have now characterized the folding pathway under near-physiological conditions. We observe that compaction of the RNA proceeds slowly to completion, even at low magnesium concentration (3 mM). Kinetic analysis shows that this compact species is a "near-native" intermediate state that is readily chased into the native state by the addition of high salt. Structural probing reveals that the near-native state represents a compact domain 1 scaffold that is not yet docked with the catalytic domains (D3 and D5). Interestingly, native ribozyme reverts to the near-native state upon reduction in magnesium concentration. Therefore, while the intron can sustain the intermediate state under physiological conditions, the native structure is not maintained and is likely to require stabilization by protein cofactors in vivo.

Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy

The ever-increasing cellular roles ascribed to RNA raise fundamental questions regarding how a biopolymer composed of only four chemically similar building-block nucleotides achieves such functional diversity. Here, I discuss how RNA achieves added mechanistic and chemical complexity by undergoing highly controlled conformational changes in response to a variety of cellular signals. I examine pathways for achieving selectivity in these conformational changes that rely to different extents on the structure and dynamics of RNA. Finally, I review solution-state NMR techniques that can be used to characterize RNA structural dynamics and its relationship to function.

Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo

RNA loop–loop interactions are a prevalent motif in the formation of tertiary structure and are well suited to trigger molecular recognition between RNA molecules. We determined the stabilities of several loop–loop interactions with a constant 6 bp core sequence and varying unpaired flanking nucleotides and found that the flanking bases have a strong influence on the stability and ion dependence of the kissing complex. In general, the stabilities determined in 1 M Na⁺ are equivalent to those in the presence of near physiological Mg²⁺ concentrations. Therefore we further tested whether the stabilities determined in vitro and within yeast cells correlate, using a recently developed yeast RNA-hybrid system. For the majority of the loop types analyzed here, the melting temperatures determined in vitro are in good agreement with the relative β-galactosidase activity in yeast cells, showing that data derived from in vitro measurements reflect in vivo properties. The most stable interactions are the naturally occurring HIV-1 DIS MAL and LAI derived loops with the motif (5′ A^A/_GN₆A 3′), emphasizing the crucial role of stable kissing complexes in HIV genome dimerization.

Atomic level architecture of group I introns revealed

Twenty-two years after their discovery as ribozymes, the self-splicing group I introns are finally disclosing their architecture at the atomic level. The crystal structures of three group I introns solved at moderately high resolution (3.1-3.8A) reveal a remarkably conserved catalytic core bound to the metal ions required for activity. The structure of the core is stabilized by an intron-specific set of long-range interactions that involves peripheral elements. Group I intron structures thus provide much awaited and extremely valuable snapshots of how these ribozymes coordinate substrate binding and catalysis.

A peripheral element assembles the compact core structure essential for group I intron self-splicing

The presence of non-conserved peripheral elements in all naturally occurring group I introns underline their importance in ensuring the natural intron function. Recently, we reported that some peripheral elements are conserved in group I introns of IE subgroup. Using self-splicing activity as a readout, our initial screening revealed that one such conserved peripheral elements, P2.1, is mainly required to fold the catalytically active structure of the Candida ribozyme, an IE intron. Unexpectedly, the essential function of P2.1 resides in a sequence-conserved short stem of P2.1 but not in a long-range interaction associated with the loop of P2.1 that stabilizes the ribozyme structure. The P2.1 stem is indispensable in folding the compact ribozyme core, most probably by forming a triple helical interaction with two core helices, P3 and P6. Surprisingly, although the ribozyme lacking the P2.1 stem renders a loosely folded core and the loss of self-splicing activity requires two consecutive transesterifications, the mutant ribozyme efficiently catalyzes the first transesterification reaction. These results suggest that the intron self-splicing demands much more ordered structure than does one independent transesterification, highlighting that the universally present peripheral elements achieve their functional importance by enabling the highly ordered structure through diverse tertiary interactions.

Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA

Proteins with RNA chaperone activity are able to promote folding of RNA molecules by loosening their structure. This RNA unfolding activity is beneficial when resolving misfolded RNA conformations, but could be detrimental to RNAs with low thermodynamic stability. In order to test this idea, we constructed various RNAs with different structural stabilities derived from the thymidylate synthase (td) group I intron and measured the effect of StpA, an Escherichia coli protein with RNA chaperone activity, on their splicing activity in vivo and in vitro. While StpA promotes splicing of the wild-type td intron and of mutants with wild-type-like stability, splicing of mutants with a lower structural stability is reduced in the presence of StpA. In contrast, splicing of an intron mutant, which is not destabilized but which displays a reduced population of correctly folded RNAs, is promoted by StpA. The sensitivity of an RNA towards StpA correlates with its structural stability. By lowering the temperature to 25°C, a temperature at which the structure of these mutants becomes more stable, StpA is again able to stimulate splicing. These observations clearly suggest that the structural stability of an RNA determines whether the RNA chaperone activity of StpA is beneficial to folding.

Strategies for RNA folding and assembly

RNA is structurally very flexible, which provides the basis for its functional diversity. An RNA molecule can often adopt different conformations, which enables the regulation of its function through folding. Proteins help RNAs reach their functionally active conformation by increasing their structural stability or by chaperoning the folding process. Large, dynamic RNA-protein complexes, such as the ribosome or the spliceosome, require numerous proteins that coordinate conformational switches of the RNA components during assembly and during their respective activities.

Imperfect CAG repeats form diverse structures in SCA1 transcripts

The expanded CAG repeat in the coding sequence of the spinocerebellar ataxia type 1 (SCA1) gene is responsible for SCA1, one of the hereditary human neurodegenerative diseases. In the normal SCA1 alleles usually 1-3 CAT triplets break the continuity of the CAG repeat tracts. Here we show what is the structural role of the CAU interruptions in the SCA1 transcripts. Depending on their number and localization within the repeat tract the interruptions either enlarge the terminal loop of the hairpin formed by the repeats, nucleate the internal loops in its stem structure, or force the repeats to fold into two smaller hairpins. Thus, the interruptions destabilize the CAG repeat hairpin, which is likely to decrease its ability to participate in the putative RNA pathogenesis mechanism driven by the long CAG repeat hairpins.

Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron

Although the active site of group I introns is phylogenetically conserved, subclasses of introns have evolved different mechanisms of stabilizing the catalytic core. Large introns contain weakly conserved 'peripheral' domains that buttress the core through predicted interhelical contacts, while smaller introns use loop-helix interactions for stability. In all cases, specific and non-specific magnesium ion binding accompanies folding into the active structure. Whether similar RNA-RNA and RNA-magnesium ion contacts play related functional roles in different introns is not clear, particularly since it can be difficult to distinguish interactions directly involved in catalysis from those important for RNA folding. Using phosphorothioate interference with RNA activity and structure in the small (249 nt) group I intron from Anabaena, we used two independent assays to detect backbone phosphates important for catalysis and those involved in intron folding. Comparison of the interference sites identified in each assay shows that positions affecting catalysis cluster primarily in the conserved core of the intron, consistent with conservation of functionally important phosphates, many of which are magnesium ion binding sites, in diverse group I introns, including those from Azoarcus and Tetrahymena. However, unique sites of folding interference located outside the catalytic core imply that different group I introns, even within the same subclass, use distinct sets of tertiary interactions to stabilize the structure of the catalytic core.

The Neurospora crassa CYT-18 protein C-terminal RNA-binding domain helps stabilize interdomain tertiary interactions in group I introns

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) promotes the splicing of group I introns by stabilizing the catalytically active RNA structure. To accomplish this, CYT-18 recognizes conserved structural features of group I intron RNAs using regions of the N-terminal nucleotide-binding fold, intermediate alpha-helical, and C-terminal RNA-binding domains that also function in binding tRNA(Tyr). Curiously, whereas the splicing of the N. crassa mitochondrial large subunit rRNA intron is completely dependent on CYT-18's C-terminal RNA-binding domain, all other group I introns tested thus far are spliced efficiently by a truncated protein lacking this domain. To investigate the function of the C-terminal domain, we used an Escherichia coli genetic assay to isolate mutants of the Saccharomyces cerevisiae mitochondrial large subunit rRNA and phage T4 td introns that can be spliced in vivo by the wild-type CYT-18 protein, but not by the C-terminally truncated protein. Mutations that result in dependence on CYT-18's C-terminal domain include those disrupting two long-range GNRA tetraloop/receptor interactions: L2-P8, which helps position the P1 helix containing the 5'-splice site, and L9-P5, which helps establish the correct relative orientation of the P4-P6 and P3-P9 domains of the group I intron catalytic core. Our results indicate that different structural mutations in group I intron RNAs can result in dependence on different regions of CYT-18 for RNA splicing.

RNA folding: models and perspectives

Intrinsic events during RNA folding include conformational search and metal ion binding. Several experimentally testable models have been proposed to explain how large ribozymes accomplish folding. Future challenges include the validation of these models, and the correlation of experimental results and theoretical simulations.

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA(ile). Base pairing of the ribozyme core requires 10-fold less Mg(2+) than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37 degrees C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4-P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.

Ribozymes: the first 20 years

Twenty years have passed since the first reports that certain RNAs mediate self-splicing and precursor tRNA processing reactions in the absence of proteins. An entire field emerged to learn how RNAs that lack the chemical versatility of amino acids nonetheless assemble into enzymes that accelerate chemical reactions with efficiencies that rival those of their protein counterparts.

RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo

Efficient splicing of the td group I intron in vivo is dependent on the ribosome. In the absence of translation, the pre-mRNA is trapped in nonnative-splicing-incompetent conformations. Alternatively, folding of the pre-mRNA can be promoted by the RNA chaperone StpA or by the group I intron-specific splicing factor Cyt-18. To understand the mechanism of action of RNA chaperones, we probed the impact of StpA on the structure of the td intron in vivo. Our data suggest that StpA loosens tertiary interactions. The most prominent structural change was the opening of the base triples, which are involved in the correct orientation of the two major intron core domains. In line with the destabilizing activity of StpA, splicing of mutant introns with a reduced structural stability is sensitive to StpA. In contrast, Cyt-18 strengthens tertiary contacts, thereby rescuing splicing of structurally compromised td mutants in vivo. Our data provide direct evidence for protein-induced conformational changes within catalytic RNA in vivo. Whereas StpA resolves tertiary contacts enabling the RNA to refold, Cyt-18 contributes to the overall compactness of the td intron in vivo.