G-ribo: a new structural motif in ribosomal RNA

Analysis of the available crystal structures of the ribosome and of its subunits has revealed a new RNA motif that we call G-ribo. The motif consists of two double helices positioned side-by-side and connected by an unpaired region. The juxtaposition of the two helices is kept by a complex system of tertiary interactions spread over several layers of stacked nucleotides. In the center of this arrangement, the ribose of a nucleotide from one helix is specifically packed with the ribose and the minor-groove edge of a guanosine from the other helix. In total, we found eight G-ribo motifs in both ribosomal subunits. The location of these motifs suggests that at least some of them play an important role in the formation of the ribosome structure and/or in its function.     

An NMR and mutational study of the pseudoknot within the gene 32 mRNA of bacteriophage T2: insights into a family of structurally related RNA pseudoknots.

NMR methods were used to investigate a series of mutants of the pseudoknot within the gene 32 messenger RNA of bacteriophage T2, for the purpose of investigating the range of sequences, stem and loop lengths that can form a similar pseudoknot structure. This information is of particular relevance since the T2 pseudoknot has been considered a representative of a large family of RNA pseudoknots related by a common structural motif, previously referred to as 'common pseudoknot motif 1' or CPK1. In the work presented here, a mutated sequence with the potential to form a pseudoknot with a 6 bp stem2 was shown to adopt a pseudoknot structure similar to that of the wild-type sequence. This result is significant in that it demonstrates that pseudoknots with 6 bp in stem2 and a single nucleotide in loop1 are indeed feasible. Mutated sequences with the potential to form pseudoknots with either 5 or 8 bp in stem2 yielded NMR spectra that could not confirm the formation of a pseudoknot structure. Replacing the adenosine nucleotide in loop1 of the wild-type pseudoknot with any one of G, C or U did not significantly alter the pseudoknot structure. Taken together, the results of this study provide support for the existence of a family of similarly structured pseudoknots with two coaxially stacked stems, either 6 or 7 bp in stem2, and a single nucleotide in loop1. This family includes many of the pseudoknots predicted to occur downstream of the frameshift or readthrough sites in a significant number of viral RNAs.     

The UA_handle: a versatile submotif in stable RNA architectures

Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5′XU/AN_nX3′). It consists of a U:A Watson–Crick: Hoogsteen trans base pair stacked over a classic Watson–Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.     

Viral RNA pseudoknots: versatile motifs in gene expression and replication

RNA pseudoknots are structural elements found in almost all classes of RNA. First recognized in the genomes of plant viruses, they are now established as a widespread motif with diverse functions in various biological processes. This Review focuses on viral pseudoknots and their role in virus gene expression and genome replication. Although emphasis is placed on those well defined pseudoknots that are involved in unusual mechanisms of viral translational initiation and elongation, the broader roles of pseudoknots are also discussed, including comparisons with relevant cellular counterparts. The relationship between RNA pseudoknot structure and function is also addressed.     

RNA Structure and Stability

RNA molecules fold into specific base-paired conformations that contain single-stranded regions, A-form double helices, hairpin loops, internal loops, bulges, junctions, pseudoknots, kissing hairpins, and so forth. These structural motifs are recognized by proteins, other RNAs, and other parts of the same RNA. The interactions of these structural elements are crucial to the biological functions of the RNA molecules. We describe the different motifs and discuss their thermodynamic stabilities relative to single strands of RNA. The stabilities determine under what conditions they occur and whether they change when interacting with proteins or other ligands.     

GU receptors of double helices mediate tRNA movement in the ribosome

A new RNA structural motif consisting of two double helices closely packed via minor grooves is found in many places in the ribosome structure. The packing requires that a GU base pair in one helix be packed against a Watson-Crick pair in the other helix. Two such motifs mediate the interaction of the P- and E-tRNA with the large ribosomal subunit. Analysis of the particular positions of these two motifs in view of the available data on occupancy of tRNA-binding sites and structural changes in the ribosome during the elongation cycle suggests a distinct role for each motif in tRNA translocation.     

Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif

To understand the role of structural elements of RNA pseudoknots in controlling the extent of -1-type ribosomal frameshifting, we determined the crystal structure of a high-efficiency frameshifting mutant of the pseudoknot from potato leaf roll virus (PLRV). Correlations of the structure with available in vitro frameshifting data for PLRV pseudoknot mutants implicate sequence and length of a stem-loop linker as modulators of frameshifting efficiency. Although the sequences and overall structures of the RNA pseudoknots from PLRV and beet western yellow virus (BWYV) are similar, nucleotide deletions in the linker and adjacent minor groove loop abolish frameshifting only with the latter. Conversely, mutant PLRV pseudoknots with up to four nucleotides deleted in this region exhibit nearly wild-type frameshifting efficiencies. The crystal structure helps rationalize the different tolerances for deletions in the PLRV and BWYV RNAs, and we have used it to build a three-dimensional model of the PRLV pseudoknot with a four-nucleotide deletion. The resulting structure defines a minimal RNA pseudoknot motif composed of 22 nucleotides capable of stimulating -1-type ribosomal frameshifts.     

Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA

The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions and for base covariation revealed that in most eukaryotes the secondary structure of the area consists of 11 helices and includes two pseudoknots. In one of the pseudoknots, exchange of base pairs between the two stems seems to occur, and covariation analysis points to the presence of a base triple. The area also contains three potential insertion points where additional hairpins or branched structures are present in a number of taxa scattered throughout the eukaryotic domain.     

Pseudoknots: a new motif in the RNA game.

In the last few years a novel RNA folding principle called pseudoknotting has emerged. Originally discovered in noncoding regions of plant viral RNAs, pseudoknots now appear to be a widespread structural motif in a number of functionally different RNAs. These structural elements are part of tRNA-like structures and are involved in folding catalytic sites of ribozymes. They increase the efficiency of ribosomal frameshifting or can serve as specific binding sites for regulatory proteins.     

Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome

To understand how the nucleotide sequence of ribosomal RNA determines its tertiary structure, we developed a new approach for identification of those features of rRNA sequence that are responsible for formation of different short- and long-range interactions. The approach is based on the co-analysis of several examples of a particular recurrent RNA motif. For different cases of the motif, we design combinatorial gene libraries in which equivalent nucleotide positions are randomized. Through in vivo expression of the designed libraries we select those variants that provide for functional ribosomes. Then, analysis of the nucleotide sequences of the selected clones would allow us to determine the sequence constraints imposed on each case of the motif. The constraints shared by all cases are interpreted as providing for the integrity of the motif, while those ones specific for individual cases would enable the motif to fit into the particular structural context. Here we demonstrate the validity of this approach for three examples of the so-called along-groove packing motif found in different parts of ribosomal RNA.     

A new method to predict the consensus secondary structure of a set of unaligned RNA sequences

MOTIVATION: To predict the consensus secondary structure, possibly including pseudoknots, of a set of RNA unaligned sequences. RESULTS: We have designed a method based on a new representation of any RNA secondary structure as a set of structural relationships between the helices of the structure. We refer to this representation as a structural pattern. In a first step, we use thermodynamic parameters to select, for each sequence, the best secondary structures according to energy minimization and we represent each of them using its corresponding structural pattern. In a second step, we search for the repeated structural patterns, i.e. the largest structural patterns that occur in at least one sequence, i.e. included in at least one of the structural patterns associated to each sequence. Thanks to an efficient encoding of structural patterns, this search comes down to identifying the largest repeated word suffixes in a dictionary. In a third step, we compute the plausibility of each repeated structural pattern by checking if it occurs more frequently in the studied sequences than in random RNA sequences. We then suppose that the consensus secondary structure corresponds to the repeated structural pattern that displays the highest plausibility. We present several experiments concerning tRNA, fragments of 16S rRNA and 10Sa RNA (including pseudoknots); in each of them, we found the putative consensus secondary structure.     

Identifying complete RNA structural ensembles including pseudoknots

The close relationship between RNA structure and function underlines the significance of accurately predicting RNA structures from sequence information. Structural topologies such as pseudoknots are of particular interest due to their ubiquity and direct involvement in RNA function, but identifying pseudoknots is a computationally challenging problem and existing heuristic approaches usually perform poorly for RNA sequences of even a few hundred bases. We survey the performance of pseudoknot prediction methods on a data set of full-length RNA sequences representing varied sequence lengths, and biological RNA classes such as RNase P RNA, Group I Intron, tmRNA and tRNA. Pseudoknot prediction methods are compared with minimum free energy and suboptimal secondary structure prediction methods in terms of correct base-pairs, stems and pseudoknots and we find that the ensemble of suboptimal structure predictions succeeds in identifying correct structural elements in RNA that are usually missed in MFE and pseudoknot predictions. We propose a strategy to identify a comprehensive set of non-redundant stems in the suboptimal structure space of a RNA molecule by applying heuristics that reduce the structural redundancy of the predicted suboptimal structures by merging slightly varying stems that are predicted to form in local sequence regions. This reduced-redundancy set of structural elements consistently outperforms more specialized approaches.in data sets. Thus, the suboptimal folding space can be used to represent the structural diversity of an RNA molecule more comprehensively than optimal structure prediction approaches alone.     

PseudoViewer: automatic visualization of RNA pseudoknots

MOTIVATION: Several algorithms have been developed for drawing RNA secondary structures, however none of these can be used to draw RNA pseudoknot structures. In the sense of graph theory, a drawing of RNA secondary structures is a tree, whereas a drawing of RNA pseudoknots is a graph with inner cycles within a pseudoknot as well as possible outer cycles formed between a pseudoknot and other structural elements. Thus, RNA pseudoknots are more difficult to visualize than RNA secondary structures. Since no automatic method for drawing RNA pseudoknots exists, visualizing RNA pseudoknots relies on significant amount of manual work and does not yield satisfactory results. The task of visualizing RNA pseudoknots by hand becomes more challenging as the size and complexity of the RNA pseudoknots increase. RESULTS: We have developed a new representation and an algorithm for drawing H-type pseudoknots with RNA secondary structures. Compared to existing representations of H-type pseudoknots, the new representation ensures uniform and clear drawings with no edge crossing for any H-type pseudoknots. To the best of our knowledge, this is the first algorithm for automatically drawing RNA pseudoknots with RNA secondary structures. The algorithm has been implemented in a Java program, which can be executed on any computing system. Experimental results demonstrate that the algorithm generates an aesthetically pleasing drawing of all H-type pseudoknots. The results have also shown that the drawing has high readability, enabling the user to quickly and easily recognize the whole RNA structure as well as the pseudoknots themselves.     

The computer simulation of RNA folding involving pseudoknot formation.

The algorithm and the program for the prediction of RNA secondary structure with pseudoknot formation have been proposed. The algorithm simulates stepwise folding by generating random structures using Monte Carlo method, followed by the selection of helices to final structure on the basis of both their probabilities of occurrence in a random structure and free energy parameters. The program versions have been tested on ribosomal RNA structures and on RNAs with pseudoknots evidenced by experimental data. It is shown that the simulation of folding during RNA synthesis improves the results. The introduction of pseudoknot formation permits to predict the pseudoknotted structures and to improve the prediction of long-range interactions. The computer program is rather fast and allows to predict the structures for long RNAs without using large memory volumes in usual personal computer.     

A Characteristic Bent Conformation of RNA Pseudoknots Promotes –1 Frameshifting during Translation of Retroviral RNA

The structures of four different RNA pseudoknots that provide one of the signals required for ribosomal frameshifting in mouse mammary tumor virus have been determined by NMR. The RNA pseudoknots have similar sequences and assume similar secondary structures, but show significantly different frameshifting efficiencies. The three-dimensional structures of one frameshifting and one non-frameshifting RNA pseudoknot had been determined previously by our group. Here we determine the structures of two new RNA pseudoknots, and relate the structures of all four pseudoknots to their frameshifting abilities. The two efficient frameshifting pseudoknots adopt characteristic bent conformations with stem 1 bending towards the major groove of stem 2. In contrast, the two poor frameshifting pseudoknots have structures very different from each other and from the efficient frameshifters. One has linear, coaxially stacked stems, the other has stems twisted and bent, but in the opposite direction to the efficient frameshifters. Changes in loop size that favor bending (shorter loops) increase frameshifting efficiency; longer loops that allow linear arrangement of the stems decrease frameshifting. Frameshifting pseudoknots in feline immunodeficiency virus and simian retrovirus have different loop sequences, but the sequences at their stem junctions imply the same bent conformation as in the mouse mammary tumor viral RNA. The requirement for a precise pseudoknot conformation for efficient frameshifting strongly implies that a specific interaction occurs between the viral RNA pseudoknot and the host protein-synthesizing machinery.     

Exclusion of RNA strands from a purine motif triple helix.

Research concerning oligonucleotide-directed triple helix formation has mainly focused on the binding of DNA oligonucleotides to duplex DNA. The participation of RNA strands in triple helices is also of interest. For the pyrimidine motif (pyrimidine.purine.pyrimidine triplets), systematic substitution of RNA for DNA in one, two, or all three triplex strands has previously been reported. For the purine motif (purine.purine.pyrimidine triplets), studies have shown only that RNA cannot bind to duplex DNA. To extend this result, we created a DNA triple helix in the purine motif and systematically replaced one, two, or all three strands with RNA. In dramatic contrast to the general accommodation of RNA strands in the pyrimidine triple helix motif, a stable triplex forms in the purine motif only when all three of the substituent strands are DNA. The lack of triplex formation among any of the other seven possible strand combinations involving RNA suggests that: (i) duplex structures containing RNA cannot be targeted by DNA oligonucleotides in the purine motif; (ii) RNA strands cannot be employed to recognize duplex DNA in the purine motif; and (iii) RNA tertiary structures are likely to contain only isolated base triplets in the purine motif.     

Improvements of the hierarchical approach for predicting RNA tertiary structure

Computational prediction of RNA tertiary structures is a significant challenge, especially for longer RNA and pseudoknots. At present it is still difficult to do this by pure all-atom molecular dynamics simulation. One of possible approaches is through hierarchical steps: from sequence to secondary structure and then to tertiary structure. Here we present improvements of two key steps of this approach, the manual adjustment of atom clashes and bond stretches and molecular dynamics refinement. We provide an energy function to find the locations of atom clashes and bond stretches and to guide their manual adjustment and a new scheme of molecular dynamics refinement using a tested combination of solvent model and the ff98 Amber force field suitable for RNA. We predicted with higher accuracy the tertiary structures of nine typical RNA molecules of lengths from 12 to 52, including hairpins, duplex helices and pseudoknots.     

基于堆积协变信息与最小自由能预测含伪结的RNA二级结构

RNA伪结预测是RNA研究的一个难点问题。文中提出一种基于堆积协变信息与最小自由能的RNA伪结预测方法。该方法使用已知结构的RNA比对序列(ClustalW比对和结构比对)测试此方法, 侧重考虑相邻碱基对之间相互作用形成的堆积协变信息, 并结合最小自由能方法对碱基配对综合评分, 通过逐步迭代求得含伪结的RNA二级结构。结果表明, 此方法能正确预测伪结, 其平均敏感性和特异性优于参考算法, 并且结构比对的预测性能比ClustalW比对的预测性能更加稳定。文中同时讨论了不同协变信息权重因子对预测性能的影响, 发现权重因子比值在l1: l2=5:1时, 预测性能达到最优。