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At least 289 records · Page 16Linked to original sources
PubMed1986

Protein modification by RNA-dependent posttranslational aminoacylation in synaptoplasm.

A soluble enzyme system that posttranslationally adds [3H]arginine to proteins in a ribosome-free preparation of guinea pig synaptoplasm is described. The reaction in synaptoplasm is inhibited by the addition of ribonuclease-A and puromycin, indicating tRNA dependence. A limited number of proteins in synaptoplasm (molecular weights of 20, 37, and 50 kilodaltons) were found to accept arginine. We suggest that RNA-dependent posttranslational amino acylation is used by the mammalian neuron for protein processing at the synaptic terminal.

Acylation↗
PubMed2002

An expanding universe of noncoding RNAs.

Noncoding RNAs (ncRNAs) have been found to have roles in a great variety of processes, including transcriptional regulation, chromosome replication, RNA processing and modification, messenger RNA stability and translation, and even protein degradation and translocation. Recent studies indicate that ncRNAs are far more abundant and important than initially imagined. These findings raise several fundamental questions: How many ncRNAs are encoded by a genome? Given the absence of a diagnostic open reading frame, how can these genes be identified? How can all the functions of ncRNAs be elucidated?

Animals↗
PubMed1995

Modification of retroviral RNA by double-stranded RNA adenosine deaminase.

In this report, we describe a recombinant provirus generated during in vitro passage that contains a short region of adenosine-to-guanosine hypermutation. The hypermutated region is restricted to complementary sequences present in the recombinant provirus. We propose that a duplex was formed in the recombinant RNA prior to reverse transcription. This duplex was a substrate for double-stranded RNA adenosine deaminase, an activity found in all cells examined that deaminates A in double-stranded RNA, converting it to inosine, which is further converted to a guanosine by reverse transcription. It appears that cis viral sequences facilitated the A-->G transitions.

Adenosine↗
PubMed2002

The 3' end formation in small RNAs.

Small RNAs are a major class of RNAs along with transfer RNAs, ribosomal RNAs, and messenger RNAs. They vary in size from less than 100 nucleotides to several thousand nucleotides and have been identified and characterized both in prokaryotes and eukaryotes. Small RNAs participate in a variety of cellular functions including regulating RNA synthesis, RNA processing, guiding modifications in RNA, and in transport of proteins. Small RNAs are generated by a series of posttranscriptional processing steps following transcription. While RNA 5' end structure, 5' cap formation, and RNA processing mechanisms have been fairly well characterized, the 3' end processing is poorly understood. Recent data point to an emerging theme in small RNAs metabolism in which the 3' end processing is mediated by the exosome, a large multienzyme complex. In addition to removal of nucleotides by the exosome, there is simultaneous rebuilding of the 3' end of some small RNA by adenylation and/or uridylation. This review presents a picture of both degradative and rebuilding reactions operative on the 3' end of some small RNA molecules in prokaryotes and eukaryotes.

Animals↗
PubMed2005

[The effect of chromatin remodeling and modification on RNA-polymerase-mediated transcription initiation].

As eukaryotes are characterized by the presence of chromatin (intricately packaged DNA), special mechanisms are required for preparing the DNA template for operation of the transcription machinery. Recently, a close association between the chromatin state and transcription was found and numerous transcription factors modifying the physical and chemical chromatin state were revealed. This review presents a brief description of transcription initiation on the DNA template within chromatin.

Animals↗
PubMedDate not supplied

Seasonal and circadian modifications in the RNA concentration in rat adrenals after swimming effort.

Variation of the adrenal RNA as a reaction to standard physical effort--30 min. of swimming daily for 5 successive days-was studied on adult male white Wistar rats in relation to the season and the hour at which the physical effort was made. The relationship between the seasonal variation and the adrenal adaptation response to swimming was followed up in the interval between March 1972 and December 1974; the circadian variation was examined at 0600, 1200, 1800 and 0000. 1. The circannual differentiation in the response to effort is expressed in the increase of the adrenal RNA concentration, statistically non-significant in spring, maximum in summer and statistically significant in autumn; in winter, the RNA concentration, by its significant decrease as against the controls, expresses an inversion of the adrenal response to effort. 2. Within a 24-hour period the increase in the adrenal RNA concentration under effort is maximum at 1800 and generally higher at night. The fundamental chronobiologic structure of the species seems to interfere significantly the adrenal adaptation to physical effort.

Adrenal Glands↗
PubMed2002

Comparative genomics and evolution of proteins involved in RNA metabolism.

RNA metabolism, broadly defined as the compendium of all processes that involve RNA, including transcription, processing and modification of transcripts, translation, RNA degradation and its regulation, is the central and most evolutionarily conserved part of cell physiology. A comprehensive, genome-wide census of all enzymatic and non-enzymatic protein domains involved in RNA metabolism was conducted by using sequence profile analysis and structural comparisons. Proteins related to RNA metabolism comprise from 3 to 11% of the complete protein repertoire in bacteria, archaea and eukaryotes, with the greatest fraction seen in parasitic bacteria with small genomes. Approximately one-half of protein domains involved in RNA metabolism are present in most, if not all, species from all three primary kingdoms and are traceable to the last universal common ancestor (LUCA). The principal features of LUCA's RNA metabolism system were reconstructed by parsimony-based evolutionary analysis of all relevant groups of orthologous proteins. This reconstruction shows that LUCA possessed not only the basal translation system, but also the principal forms of RNA modification, such as methylation, pseudouridylation and thiouridylation, as well as simple mechanisms for polyadenylation and RNA degradation. Some of these ancient domains form paralogous groups whose evolution can be traced back in time beyond LUCA, towards low-specificity proteins, which probably functioned as cofactors for ribozymes within the RNA world framework. The main lineage-specific innovations of RNA metabolism systems were identified. The most notable phase of innovation in RNA metabolism coincides with the advent of eukaryotes and was brought about by the merge of the archaeal and bacterial systems via mitochondrial endosymbiosis, but also involved emergence of several new, eukaryote-specific RNA-binding domains. Subsequent, vast expansions of these domains mark the origin of alternative splicing in animals and probably in plants. In addition to the reconstruction of the evolutionary history of RNA metabolism, this analysis produced numerous functional predictions, e.g. of previously undetected enzymes of RNA modification.

Animals↗
PubMed1995

Rp-phosphorothioate modifications in RNase P RNA that interfere with tRNA binding.

We have used Rp-phosphorothioate modifications and a binding interference assay to analyse the role of phosphate oxygens in tRNA recognition by Escherichia coli ribonuclease P (RNase P) RNA. Total (100%) Rp-phosphorothioate modification at A, C or G positions of RNase P RNA strongly impaired tRNA binding and pre-tRNA processing, while effects were less pronounced at U positions. Partially modified E. coli RNase P RNAs were separated into tRNA binding and non-binding fractions by gel retardation. Rp-phosphorothioate modifications that interfered with tRNA binding were found 5' of nucleotides A67, G68, U69, C70, C71, G72, A130, A132, A248, A249, G300, A317, A330, A352, C353 and C354. Manganese rescue at positions U69, C70, A130 and A132 identified, for the first time, sites of direct metal ion coordination in RNase P RNA. Most sites of interference are at strongly conserved nucleotides and nine reside within a long-range base-pairing interaction present in all known RNase P RNAs. In contrast to RNase P RNA, 100% Rp-phosphorothioate substitutions in tRNA showed only moderate effects on binding to RNase P RNAs from E. coli, Bacillus subtilis and Chromatium vinosum, suggesting that pro-Rp phosphate oxygens of mature tRNA contribute relatively little to the formation of the tRNA-RNase P RNA complex.

Base Sequence↗
PubMed1993

Mammalian U6 small nuclear RNA undergoes 3' end modifications within the spliceosome.

Mammalian U6 small nuclear RNA (snRNA) is heterogeneous with respect to the number of 3' terminal U residues. The major form terminates with five U residues and a 2',3' cyclic phosphate. Because of the presence in HeLa cell nuclear extracts of a terminal uridylyl transferase, a minor form of U6 snRNA is elongated, producing multiple species containing up to 12 U residues. In this study we have used glycerol gradients to demonstrate that these U6 snRNA forms are assembled into U6 ribonucleoprotein (RNP), U4/U6 snRNPs, and U4/U5/U6 tri-snRNP complexes. Furthermore, glycerol gradients combined with affinity selection of biotinylated pre-mRNAs led us to show that elongated forms of U6 snRNAs enter the spliceosome and that some of these become shortened with time to a single species having the same characteristics as the major form of U6 snRNA present in mammalian nuclear extracts. We propose that this elongation-shortening process is related to the function of U6 snRNA in mammalian pre-mRNA splicing.

Base Composition↗
PubMed1988

Poliovirus-induced modification of host cell RNA polymerase IIO is prevented by cycloheximide and zinc.

Infection of HeLa cells with poliovirus results in a decrease in the level of RNA polymerase IIO, the transcriptionally active form of the enzyme, and a shutdown of host transcription (Rangel, L. M., Fernández-Tomas, C., Dahmus, M. E., and Gariglio, P. (1987) J. Virol. 61, 1002-1006). The effect of cycloheximide on poliovirus-induced modification of host RNA polymerase IIO was investigated. The inhibition of protein synthesis, at sequential stages during viral replication, prevents the modification of both total and chromatin-bound RNA polymerase IIO. Furthermore, the inclusion of zinc at a concentration that inhibits the proteolytic post-translational processing of viral polyprotein also prevents the modification of RNA polymerase IIO. These results suggest that host cell enzyme modification depends on the synthesis and processing of protein(s) encoded by the viral genome.

Cell Transformation, Viral↗
PubMed2026

Marked for Success: How RNA m6A Methylation Fine-Tunes Gut Epithelial Function.

Post-transcriptional gene regulation-particularly through RNA modifications-plays an essential but understudied role in development, homeostasis, and regeneration of rapidly changing tissues like the mammalian intestinal epithelium. RNA modifications such as N6-methyladenosine (m⁶A) represent a burgeoning area of research in posttranscriptional regulation, with m⁶A being the most abundant modification found in approximately 25% of all mRNA transcripts. Multiple groups have begun to report m⁶A and associated regulation of mRNA fate as critical to key process in the intestinal epithelium. In this review, we synthesize key findings to date into the following 3 categories: m⁶A changes in response to the homeostatic luminal environment, m⁶A as a mediator of stemness in the crypt, and m⁶A as a tool for reacting to inflammation and injury. Over the course of this review, we will demonstrate how m⁶A is uniquely positioned to regulate homeostasis and disease states in the challenging and dynamic environment of the intestinal epithelium.

Humans↗
PubMed1976

Bacillus subtilis RNA polymerase and its modification in sporulating and phage-infected bacteria.

Bacillus subtilis RNA polymerase holoenzyme consists of the subunits beta', beta, sigma, alpha, delta, and omega. In sporulating bacteria and in bacteria infected with phages SP01 and SP82, this enzyme undergoes changes in subunit composition and transcriptional specificity that could play a regulatory role in gene transcription. Sporulating bacteria may contain a specific component that inhibits the activity of the sigma subunit of polymerase probably by interfering with the binding of sigma-polypeptide to core enzyme. The hypothetical inhibitor may be metabolically unstable, since its activity is rapidly depleted from sporulating cells in the presence of chloramphenicol. Inhibition of sigma-polypeptide activity may restrict the transcription of phage DNA an infected sporulating cells. Although lacking the sigma-subunit, RNA polymerase purified from sporulating cells contains sporulation-specific subunits of 85,000 and 27,000 daltons. In SP01-infected bacteria, the sigma-subunit is replaced by phage-induced subunits. Purified enzyme containing the protein product of SP01 regulatory gene 28 directs the transcription of phage middle genes in vitro, while enzyme containing phage-induced polypeptides V and VI preferentially copies late genes. Accurate transcription of middle and late genes in vitro requires the host delta-subunit of polymerase (or high ionic strength) but not sigma-subunit. Phage PBS2 induces an entirely new multisubunit RNA polymerase that specifically transcribes PBS2 DNA in vitro. This enzyme is synthesized de novo after infection and does not arise by modification of the B. subtilis holoenzyme.

Antigen-Antibody Reactions↗
PubMed2024

Mass Spectrometry-Based Proteomics for Assessing Epitranscriptomic Regulations.

Epitranscriptomics is a rapidly evolving field that explores chemical modifications in RNA and how they contribute to dynamic and reversible regulations of gene expression. These modifications, for example, N6-methyladenosine (m6A), are crucial in various RNA metabolic processes, including splicing, stability, subcellular localization, and translation efficiency of mRNAs. Mass spectrometry-based proteomics has become an indispensable tool in unraveling the complexities of epitranscriptomics, offering high-throughput, precise protein identification, and accurate quantification of differential protein expression. Over the past two decades, advances in mass spectrometry, including the improvement of high-resolution mass spectrometers and innovative sample preparation methods, have allowed researchers to perform in-depth analyses of epitranscriptomic regulations. This review focuses on the applications of bottom-up proteomics in the field of epitranscriptomics, particularly in identifying and quantifying epitranscriptomic reader, writer, and eraser (RWE) proteins and in characterizing their functions, posttranslational modifications, and interactions with other proteins. Together, by leveraging modern proteomics, researchers can gain deep insights into the intricate regulatory networks of RNA modifications, advancing fundamental biology, and fostering potential therapeutic applications.

Proteomics↗
PubMedDate not supplied

[Computational search for potential post-translational modification sites in human RNA polymerase III subunits].

The transcription of small stable non-translated RNA genes (class III genes), directed by RNA polymerase III, is strictly regulated in accordance to physiological state of the cell (growth rate, cell cycle stage, apoptosis, etc.) Post-translational modifications of the polymerase may play the important role in class III gene transcription regulation. Using computational programs searching for potential post-translational modifications sites in proteins (MotifScan, NetPhos 2.0, and Yin-Yan 1.2), possible sites of phosphorylation were identified in all 17 subunits of human RNA polymerase III, and possible sites of reciprocal phosphorylation and glycosilation ("yin-yan" sites) - in 13 subunits. Among the identified sites -17 sites of phosphorylation in seven subunits are conservative in human, Saccharomyces cerevisiae and Schizosaccharomyces pombe, including two "yin-yan" sites in two subunits. The data obtained can be used for experimental identification of RNA polymerase III modification sites in vivo in cells being in different physiological states.

Computational Biology↗