RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence

The double-stranded RNA binding domain (dsRBD) is a small protein domain of 65–70 amino acids adopting an αβββα fold, whose central property is to bind to double-stranded RNA (dsRNA). This domain is present in proteins implicated in many aspects of cellular life, including antiviral response, RNA editing, RNA processing, RNA transport and, last but not least, RNA silencing. Even though proteins containing dsRBDs can bind to very specific dsRNA targets in vivo, the binding of dsRBDs to dsRNA is commonly believed to be shape-dependent rather than sequence-specific. Interestingly, recent structural information on dsRNA recognition by dsRBDs opens the possibility that this domain performs a direct readout of RNA sequence in the minor groove, allowing a global reconsideration of the principles describing dsRNA recognition by dsRBDs. We review in this article the current structural and molecular knowledge on dsRBDs, emphasizing the intricate relationship between the amino acid sequence, the structure of the domain and its RNA recognition capacity. We especially focus on the molecular determinants of dsRNA recognition and describe how sequence discrimination can be achieved by this type of domain.     

Alkylation of double-stranded ribonucleic acid with 2-chloroethylamines

Zusammenfassung Nachweis der Alkylierung doppelfädiger RNS mittels 2-Chloräthylaminen in wässeriger Lösung ohne gleichzeitige Hydrolyse der Phosphatesterbindungen zwischen den Nukleotiden, was in starkem Gegensatz zu früheren, bei einfädigen RNS gewonnenen Ergebnissen steht.     

Polarographic behaviour of polycytidylic acid and its double-stranded complex with polyinosinic acid

Zusammenfassung Es ergibt sich, dass die Polyzytidylsäure unter dem neutralen pH eine polarographische Reduktionswelle ähnlich der Welle der denaturierten Desoxyribonukleinsäure gewährt. Zur Bestimmung der Polyzytidylsäure mit der «ersten Kurve» genügt bereits 1/10g des Stoffes. Im Komplex der Polyzytidylsäure mit Polyinosinsäure ist die Reduzierbarkeit der Polyzytidylsäure eliminiert.     

Microtubule associated protein tau binds to double-stranded but not single-stranded DNA

Tau, a major microtubule-associated protein of the neuron, which is known to promote the assembly of and to stabilize microtubules, has also been seen associated with chromatin in neuronal cell lines, but its role in this subcellular compartment is still unknown. In this study, the binding of tau to DNA was investigated using the electrophoretic mobility shift assay. Using polynucleotide as probe, we found that tau bound to double-stranded but not to single-stranded DNA. Formation of tau-polynucleotide complex was disrupted by alkaline pH and a high concentration of NaCl, but was not affected by dithiothreitol. Electron microscopy revealed that the protein associated with the nucleic acid in a necklacelike manner. DNA-cellulose chromatography and radioimmunodot-blot analyses showed that calf thymus histones VI-S, VII-S and VIII-S could replace both recombinant human brain tau₃₅₂ (tau-23) and tau₄₄₁ (tau-40) from DNA. Thus, tau appears to bind to DNA reversibly in the presence of histones. Received 24 November 2002; received after revision 28 December 2002; accepted 30 December 2002 RID="*" ID="*"Corresponding author.     

RNA processing and human disease

Gene expression involves multiple regulated steps leading from gene to active protein. Many of these steps involve some aspect of RNA processing. Diseases caused by mutations that directly affect RNA processing are relatively rare compared with mutations that disrupt protein function. The vast majority of diseases of RNA processing result from loss of function of a single gene due to mutations in cis-acting elements required for pre-messenger RNA (mRNA) splicing. However, a few diseases are caused by alterations in the trans-acting factors required for RNA processing and in the vast majority of cases it is the pre-mRNA splicing machinery that is affected. Clearly, alterations that disrupt splicing of pre-mRNAs from large numbers of genes would be lethal at the cellular level. A common theme among these diseases is that only subsets of genes are affected. This is consistent with an emerging view that different subsets of exons require different sets of cis-acting elements and trans-acting factors.     

RNA uridylyltransferases

The terminal RNA uridylyltransferases (TUTases) catalyze transfer of UMP residues to the 3' hydroxyl group of RNA. These activities are widespread among eukaryotes and appear to be involved in a variety of RNA-processing pathways. Recent studies of RNA editing in trypanosomatids have provided the first insights into the biological functions of RNA uridylyltransferases, which had eluded biochemical identification despite 30-year-old evidence of such activities in mammals and plants. Comparative sequence analysis of trypanosomal TUTases and their homologs revealed by large-scale genomic projects demonstrates a significant level of biochemical and structural diversity between putative uridylyltransferases. The conserved catalytic domain has acquired additional protein modules and appears to have adapted to perform functionally distinct tasks of guided U-insertion into mRNA and constrained addition of an oligo[U] tail to guide RNAs. Here I discuss the current knowledge of this novel enzyme family and possible roles of RNA uridylylation in the regulation of gene expression.     

Crystallization of RNA

Even as the number of RNA structures determined and under study multiplies, the critical step in X-ray diffraction analysis, growth of single well-ordered crystals, remains at the boundary between art and science. Recent advances in methods of RNA synthesis, purification, and characterization, as well as empirical and technical improvements in crystallization techniques, the development of cryo-crystallography, and the wider availability of bright, tunable, X-rays from synchrotron sources are improving the chances of obtaining RNA crystals suitable for X-ray structural analysis. In this review, we summarize the current status of the design, preparation, purification, and analysis of RNA for crystallization and describe the latest approaches to obtaining diffraction-quality crystals. Received 17 October 2000; revised 6 December 2000; accepted 8 December 2000     

Aging in relation to auxin and RNA

Résumé Sur des extraits de racine deLens culinaris, il est observé qu'au cours du vieillissement cellulaire les enzymes qui contrôlent le catabolisme auxinique sont progressivement plus actives, ce qui a pour conséquence d'entraîner une diminution du taux en auxines endogènes. Par ailleurs, l'activité des systèmes RNasiques — inhibés par les auxines — va s'élever d'une façon significative dans les cellules âgées ce qui explique, partiellement du moins, la diminution de le teneur en RNA.     

Stress and the nonsense-mediated RNA decay pathway

Cells respond to internal and external cellular stressors by activating stress-response pathways that re-establish homeostasis. If homeostasis is not achieved in a timely manner, stress pathways trigger programmed cell death (apoptosis) to preserve organism integrity. A highly conserved stress pathway is the unfolded protein response (UPR), which senses excessive amounts of unfolded proteins in the ER. While a physiologically beneficial pathway, the UPR requires tight regulation to provide a beneficial outcome and avoid deleterious consequences. Recent work has demonstrated that a conserved and highly selective RNA degradation pathway—nonsense-mediated RNA decay (NMD)—serves as a major regulator of the UPR pathway. NMD degrades mRNAs encoding UPR components to prevent UPR activation in response to innocuous ER stress. In response to strong ER stress, NMD is inhibited by the UPR to allow for a full-magnitude UPR response. Recent studies have indicated that NMD also has other stress-related functions, including promoting the timely termination of the UPR to avoid apoptosis; NMD also regulates responses to non-ER stressors, including hypoxia, amino-acid deprivation, and pathogen infection. NMD regulates stress responses in species across the phylogenetic scale, suggesting that it has conserved roles in shaping stress responses. Stress pathways are frequently constitutively activated or dysregulated in human disease, raising the possibility that “NMD therapy” may provide clinical benefit by downmodulating stress responses.     

RNA induced anti-kidney auto-antibodies

Riassunto Sono stati descritti alcuni aspetti funzionali, morfologici ed istoimmunochimici di una nefropatia sperimentalmente indotta nel ratto mediante l'uso di un RNA estratto da siero e da tessuto linfoide di conigli immunizzati con antigeni renali di ratto.     

Re-creating an RNA world

The RNA world hypothesis states that life originated via a system based on RNA genomes and RNA catalysts. Researchers have been trying to develop such a system since catalytic RNAs (ribozymes) were discovered in 1982. This review summarizes the recent progress made in that endeavor and outlines the obstacles that remain to be overcome. After giving a short background on prebiotic chemistry and in vitro evolution, the discussion focuses on the generation of three important components of an RNA world: a sufficient polymerase ribozyme, self-replicating membrane compartments and ribozymes that are capable of performing basic metabolic processes. Received 31 January 2006; accepted 15 March 2006     

DNA and RNA content in diploid and tetraploid amphibians

Resumen En el anuro tetraploide naturalOdontophrynus americanus, el contenido de DNA es el doble que el determinado, bioquimicamente, en los especimens de la población diploide deO. americanus. Sin embargo el contenido de RNA de ejemplares de las dos poblaciones es aproximadamente igual. Aparentemente, mecanismos de regulación bloquean el esceso de material genético en el tetraploide.

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This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo, the Conselho Nacional de Pesquisas, the Fundo de Pesquisas do Instituto Butantan and the Rockefeller Foundation.