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PubMed2002

Elongation by RNA polymerase II: structure-function relationship.

RNA polymerase II is the eukaryotic enzyme that transcribes all the mRNA in the cell. Complex mechanisms of transcription and its regulation underlie basic functions including differentiation and morphogenesis. Recent evidence indicates the process of RNA chain elongation as a key step in transcription control. Elongation was therefore expected and found to be linked to human diseases. For these reasons, major efforts in determining the structures of RNA polymerases from yeast and bacteria, at rest and as active enzymes, were undertaken. These studies have revealed much information regarding the processes involved in transcription. Eukaryotic RNA polymerases and their homologous bacterial counterparts are flexible enzymes with domains that separate DNA and RNA, prevent the escape of nucleic acids during transcription, allow for extended pausing or "arrest" during elongation, allow for translocation of the DNA and more. Structural studies of RNA polymerases are described below within the context of the process of transcription elongation, its regulation and function.

Bacteria↗
PubMed2002

The accuracy of ribosomal RNA comparative structure models.

The determination of the 16S and 23S rRNA secondary structure models was initiated shortly after the first complete 16S and 23S rRNA sequences were determined in the late 1970s. The structures that are common to all 16S rRNAs and all 23S rRNAs were determined using comparative methods from the analysis of thousands of rRNA sequences. Twenty-plus years later, the 16S and 23S rRNA comparative structure models have been evaluated against the recently determined high-resolution crystal structures of the 30S and 50S ribosomal subunits. Nearly all of the predicted covariation-based base pairs, including the regular base pairs and helices, and the irregular base pairs and tertiary interactions, were present in the 30S and 50S crystal structures.

Crystallography, X-Ray↗
PubMed2004

The splicing of yeast mitochondrial group I and group II introns requires a DEAD-box protein with RNA chaperone function.

Group I and II introns self-splice in vitro, but require proteins for efficient splicing in vivo, to stabilize the catalytically active RNA structure. Recent studies showed that the splicing of some Neurospora crassa mitochondrial group I introns additionally requires a DEAD-box protein, CYT-19, which acts as an RNA chaperone to resolve nonnative structures formed during RNA folding. Here we show that, in Saccharomyces cerevisiae mitochondria, a related DEAD-box protein, Mss116p, is required for the efficient splicing of all group I and II introns, some RNA end-processing reactions, and translation of a subset of mRNAs, and that all these defects can be partially or completely suppressed by the expression of CYT-19. Results for the aI2 group II intron indicate that Mss116p is needed after binding the intron-encoded maturase, likely for the disruption of stable but inactive RNA structures. Our results suggest that both group I and II introns are prone to kinetic traps in RNA folding in vivo and that the splicing of both types of introns may require DEAD-box proteins that function as RNA chaperones.

Amino Acid Motifs↗
PubMed1993

The beet western yellows virus ST9-associated RNA shares structural and nucleotide sequence homology with carmo-like viruses.

Complementary DNAs corresponding to the virion RNAs of the ST9 isolate of beet western yellows virus (ST9 BWYV) were cloned and the complete, 2843 nucleotide sequence of a unique RNA associated with ST9 BWYV, the ST9-associated RNA (ST9 aRNA), was determined. Three ORFs with deduced translation products of molecular weights 22,600, 12,500, and 35,900, respectively, and a small ORF, potentially encoding for a 3400 molecular weight protein, were identified in the ST9 aRNA sequence. Possible gene products of the ST9 aRNA were identified by in vitro translation analysis of the ST9 BWYV virion RNAs (the ST9 BWYV genomic RNA [ST9 BWYV gRNA] and the ST9 aRNA) and of transcripts representing the nearly full-length ST9 aRNA, individual ORFs, and specific ORF combinations. Proteins of 23,000 and 28,000 M(r) were derived from ORF 1 transcripts, while proteins of 25,000 and 35,000 M(r) were derived from ORF 3 transcripts. Larger proteins of 85,000 and 45,000 M(r) were also identified, and shown to possibly arise by continuous translation of ORFs 1, 2, and 3 (by possible readthrough and frameshift), or ORFs 2 and 3 (by possible frameshift), respectively. No products were detected from transcripts representing only ORF 2. Computer database searches and analyses indicated that the ST9 aRNA shares significant nucleotide sequence homology with carmo-like viruses, but not with its helper virus, BWYV. Amino acid sequence analyses also indicated that the ST9 aRNA ORF 2 and ORF 3 regions share extensive homology with putative RNA-dependent RNA polymerases of carmo-like viruses.

Amino Acid Sequence↗
PubMed1999

[Computerized ribosomal RNA secondary structure modeling of mutants found in Rett syndrome patients and their mothers].

OBJECTIVE: To identify the secondary structure of rRNA mutants, mtDNA2835(C-->T) and mtDNA2706(A-->G) found in Rett syndrome patients and their mothers. METHODS: Both wild type mtDNA sequence of rRNA gene and mutated sequence were input into computer (converted into RNA sequences) and analyzed by the sofware DNASIS v6. 14. The unique prediction size is set 300 bases and the maximum bulge and interior loop size,30 bases. RESULTS: Similar to the positive controls, the mtDNA2835(C-->T) made the 16S rRNA secondary structure totally different,and the energy changes a lot. On the contrary, the mtDNA2706(A-->G) altered little of secondary structure with a small energy shift. CONCLUSION: Computerized folding programs have provided us with a quick prediction of rRNA structure changes induced by these two mutations. Of them, the mtDNA2835(C-->T) might relate to the pathogenesis of Rett syndrome, but the mtDNA2706(A--> G) might be less meaningful.

Computer Simulation↗
PubMed2002

Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences.

The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in bacilli by binding to the leader region of the nascent trp operon mRNA. When activated by binding tryptophan, the 11-subunit circular TRAP molecule binds to a target sequence consisting of 11 (G/U)AG repeats, separated by two or three variable 'spacer' nucleotides. Reported here are two crystal structures of TRAP bound to RNAs containing 11 GAG repeats separated by UU and CC spacer nucleotides, determined at 1.75 and 2.50 A resolution, respectively. These show the spacer regions of the RNA molecules to be highly flexible, making no direct hydrogen-bonding contacts with the protein. Comparison of these structures with the previous structure of TRAP bound to (GAGAU)(10)GAG RNA, in which the spacer nucleotides stack with each other close to the protein surface, shows that the RNA can adopt different conformations depending on the sequence of the spacer regions. This gives insight into the structural basis of the specificity of TRAP and into the mechanism of binding.

Bacterial Proteins↗
PubMed2004

Riboswitches exert genetic control through metabolite-induced conformational change.

Conserved RNA structures have traditionally been thought of as potential binding sites for protein factors and consequently are regarded as fulfilling relatively passive albeit important roles in cellular processes. With the discovery of riboswitches, RNA no longer takes a backseat to protein when it comes to affecting gene expression. Riboswitches bind directly to cellular metabolites with exceptional specificity and affinity, and exert control over gene expression through ligand-induced conformational changes in RNA structure. Riboswitches now represent a widespread mechanism by which cells monitor their metabolic state and facilely alter gene expression in response to changing conditions.

Gene Expression Regulation↗
PubMed2006

Hairpin RNA: a secondary structure of primary importance.

An RNA hairpin is an essential secondary structure of RNA. It can guide RNA folding, determine interactions in a ribozyme, protect messenger RNA (mRNA) from degradation, serve as a recognition motif for RNA binding proteins or act as a substrate for enzymatic reactions. In this review, we have focused on cis-acting RNA hairpins in metazoa, which regulate histone gene expression, mRNA localization and translation. We also review evolution, mechanism of action and experimental use of trans-acting microRNAs, which are coded by short RNA hairpins. Finally, we discuss the existence and effects of long RNA hairpin in animals. We show that several proteins previously recognized to play a role in a specific RNA stem-loop function in cis were also linked to RNA silencing pathways where a different type of hairpin acts in trans. Such overlaps indicate that the relationship between certain mechanisms that recognize different types of RNA hairpins is closer than previously thought.

Animals↗
PubMed2005

Discontinuous subgenomic RNA synthesis in arteriviruses is guided by an RNA hairpin structure located in the genomic leader region.

Nidoviruses produce an extensive 3'-coterminal nested set of subgenomic (sg) mRNAs, which are used to express structural proteins and sometimes accessory proteins. In arteriviruses and coronaviruses, these mRNAs contain a common 5' leader sequence, derived from the genomic 5' end. The joining of the leader sequence to different segments derived from the 3'-proximal part of the genome (mRNA bodies) presumably involves a unique mechanism of discontinuous minus-strand RNA synthesis in which base pairing between sense and antisense transcription-regulating sequences (TRSs) plays an essential role. The leader TRS is present in the loop of a hairpin structure that functions in sg mRNA synthesis. In this study, the minimal sequences in the 5'-proximal region of the Equine arteritis virus genome that are required for sg RNA synthesis were delimited through mutagenesis. A full-length cDNA clone was engineered in which this domain was duplicated, allowing us to make mutations and monitor their effects on sg RNA synthesis without seriously affecting genome replication and translation. The leader TRS present in the duplicated sequence was used and yielded novel sg mRNAs with significantly extended leaders. Our combined findings suggest that the leader TRS hairpin (LTH) and its immediate flanking sequences are essential for efficient sg RNA synthesis and form an independent functional entity that could be moved 300 nucleotides downstream of its original position in the genome. We hypothesize that a conformational switch in the LTH region regulates the role of the 5'-proximal region of the arterivirus genome in subgenomic RNA synthesis.

Base Sequence↗
PubMed1989

A new method to find a set of energetically optimal RNA secondary structures.

We present a computer method to determine nucleic acid secondary structures. It is based on three steps: 1) the search for all possible helical regions relied on a mathematical approach derived from the convolution theorem; it uses a tetradimensional complex vector representation of the bases along the sequence; 2) a 'tree' search for a set of minimum free energy structures, by the aid of an approximate energy evaluation to reduce the computer time requirements; 3) the exact calculation and refinement of the energies. A method to introduce the experimental data and reach an arrangement between them and the free energy minimization criterion is shown. In order to demonstrate the confidence of the program a test on four RNA sequences is performed. The method has computer time requirement proportional to N2, where N is the length of the sequence and retrieves a set of optimal free energy structures.

Base Composition↗
PubMed1993

A highly sensitive probe for guanine N7 in folded structures of RNA: application to tRNA(Phe) and Tetrahymena group I intron.

A nickel complex has been shown to promote conformation-specific oxidation of guanosine in polynucleotide RNA. In all cases, reaction was strictly dependent on the solvent exposure and surface properties of guanine N7. Modification of native tRNA(Phe) (yeast) was detected at G18, G19, G20, and Gm34 and concurred with predictions based on its crystal structure. Additional guanine derivatives became exposed to oxidation only after the tRNA unfolded in the absence of Mg2+. Reaction of the Tetrahymena group I intron RNA (L-21 ScaI) also compared favorably to its three-dimensional model by appropriately identifying guanosine residues in hairpin loops, duplex termini, and the essential cofactor binding site. These results complemented prior data generated by hydroxyl radical, and in combination they served to distinguish the solvent accessibility of sugar backbone and base positions in guanosine residues. Most importantly, this nickel complex exhibited greater selectivity than either dimethyl sulfate or RNase T1 for characterizing tRNA(Phe) and intron RNA.

Animals↗
PubMed2006

RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA.

The RNAKinetics server (http://www.ig-msk.ru/RNA/kinetics) is a web interface for the newly developed RNAKinetics software. The software models the dynamics of RNA secondary structure by the means of kinetic analysis of folding transitions of a growing RNA molecule. The result of the modeling is a kinetic ensemble, i.e. a collection of RNA structures that are endowed with probabilities, which depend on time. This approach gives comprehensive probabilistic description of RNA folding pathways, revealing important kinetic details that are not captured by the traditional structure prediction methods. The access to the RNAKinetics server is free.

Base Sequence↗
PubMed2004

Three properties of the hepatitis C virus RNA genome related to antiviral strategies based on RNA-therapeutics: variability, structural conformation and tRNA mimicry.

The concept of using RNA molecules as therapeutic agents is receiving increasing attention by basic science and pharmaceutical research. Over the past five years, a number of clinical trials have been initiated to evaluate the efficacy and safety of several RNA agents for the treatment of a range of conditions from cancer to infectious disease. From a molecular biology perspective, two main factors are implicated in RNA therapeutics against pathogenic RNAs: i/ The activity, stability and delivery of the inactivating agent (ribozyme, RNase P, "decoy" RNA, aptamer, small interfering-RNA) and its co-localisation with the target; and ii/ The properties of the RNA substrate, which, in the case of an RNA virus, most likely limit the effectiveness of the inactivating agent. The main reasons are the limited size of the viral genome and the restrictions imposed by the RNA structure and variations at the target. In the first section of this article we review three properties of the HCV RNA genome, from primary sequence to tertiary structure, which imply restrictions and opportunities for RNA-based treatment. In the second section, we briefly describe several of the RNA-based therapeutic strategies against HCV now under development.

5' Untranslated Regions↗
PubMed2003

Deletion of stem-loop 3 is compensated by second-site mutations within the Gag protein of human immunodeficiency virus type 1.

Encapsidation of human immunodeficiency virus type 1 (HIV-1) RNA involves specific interactions between viral Gag proteins and viral RNA elements located at the 5' untranslated region (UTR). These RNA elements are termed packaging (psi) or encapsidation (E) signals and mainly comprise the stem-loop 1 (SL1) and SL3 RNA structures. We have previously shown that deletion of the SL1 sequences is compensated by second-site mutations within Gag. Similar studies are now extended to SL3 and the results demonstrate that deletion of this RNA structure is rescued by two point mutations, i.e., A11V in p2 and I12V in nucleocapsid (NC). These two compensatory mutations are different from those associated with the rescue of SL1 deletion, suggesting that SL1 and SL3 may bind to different residues of Gag during viral RNA packaging. Analysis of virion-derived RNA in native agarose gels shows that deletion of SL3 leads to decreases in both viral RNA packaging and dimerization. These defects are corrected by the compensatory mutations A11V and I12V. Yet, defects in viral RNA dimerization at an early stage that were caused by the SL3 deletion in the context of a viral protease-negative mutation cannot be overcome by these two suppressor mutations. Therefore, the positive effects of A11V and I12V on dimerization of the SL3-deleted RNA must have taken place at the maturation stage.

Animals↗
PubMed1985

Alternative splicing caused by RNA secondary structure.

mRNA precursors with stable hairpins were constructed by inserting inverted repeats into an adenovirus transcriptional template that encoded the three late leader exons. When the loop of the hairpin contained the second exon and the flanking splice sites, most of the RNA spliced in vitro had the first exon joined directly to the third exon. The remainder was spliced normally. The same types of alternatively spliced RNAs were formed when a similar template was introduced into HeLa cells by transfection. Thus both in extracts and in cells, an exon became optional when sequestered in a hairpin loop. Perhaps a related mechanism creates the alternative splicing patterns of complex transcription units.

Adenoviruses, Human↗