Drug effects on nucleic acid modification. I. A specific effect of 5-azacytidine on mammalian transfer RNA methylation in vivo.
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Animals↗
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Modification of an essential arginine in Escherichia coli DNA-dependent RNA polymerase.
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Aldehydes↗
Photo-modification studies of the contacts of the 5'-terminus of growing RNA with the subunits of RNA-polymerase.
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Adenosine Triphosphate↗
Trace metal modification of immunocompetence. II. Effect of Pb2+, Cd2+, and Cr3+ on RNA turnover, hexokinase activity, and blastogenesis during B-lymphocyte transformation in vitro.
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Animals↗
[Recombinant components of the EcoRII restriction-modification system. Ability of restriction endonucleases to interact with DNA-RNA duplexes].
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Base Sequence↗
Effect of secondary structure of messenger ribonucleic acid on the formation of initiation complexes with prokaryotic and eukaryotic ribosomes.
The effect of modification of the secondary structure of phage f2 RNA and brome mosaic virus (BMV) RNA 3 on the formation of initiation complexes in Escherichia coli and wheat germ protein-synthesizing systems was studied. Modification of the RNAs was achieved by using O-methylhydroxylamine, which specifically reacts with cytosines; this leaves the initiation codons unchanged and, under denaturing conditions, leads to irreversible unfolding of the RNA. E. coli ribosomes interact with newly exposed AUG/GUG codons in the modified templates forming polysomes, whereas they form monosomes with native f2 RNA or BMV RNA 3. With wheat germ ribosomes, disomes are formed in the presence of BMV RNA 3, either native or modified. With f2 RNA, eukaryotic ribosomes form monosomes, independent of the secondary structure of the template. The results indicate that, in contrast to prokaryotic ribosomes, binding of eukaryotic ribosomes to f2 RNA or BMV RNA 3 is not affected by modification of the secondary structure of these messengers.
Cells↗
Novel and essential subunits in the 300-kilodalton nuclear cap binding complex of Trypanosoma brucei.
One of the unique aspects of RNA processing in trypanosomatid protozoa is the presence of a cap 4 structure (m7Gpppm2(6)AmpAmpCmpm3Um) at the 5' end of all mRNAs. The cap 4 becomes part of the mRNA through trans-splicing of a 39-nucleotide-long sequence donated by the spliced leader RNA. Although the cap 4 modifications are required for trans-splicing to occur, the underlying mechanism remains to be determined. We now describe an unconventional nuclear cap binding complex (CBC) in Trypanosoma brucei with an apparent molecular mass of 300 kDa and consisting of five protein components: the known CBC subunits CBP20 and importin-alpha and three novel proteins that are only present in organisms featuring a cap 4 structure and trans-splicing. Competitive binding studies are consistent with a specific interaction between the CBC and the cap 4 structure. Downregulation of several individual components of the T. brucei CBC by RNA interference demonstrated an essential function at an early step in trans-splicing. Thus, our studies are consistent with the CBC providing a mechanistic link between cap 4 modifications and trans-splicing.
Amino Acid Sequence↗
Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA:tRNA complex by mass spectrometry and a primary amine selective reagent.
We have devised a high-resolution protein footprinting methodology to dissect HIV-1 reverse transcriptase (RT) contacts to the viral RNA:tRNA complex. The experimental strategy included modification of surface-exposed lysines in RT and RT-viral RNA:tRNA complexes by the primary amine selective reagent NHS-biotin, SDSPAGE separation of p66 and p51 polypeptides, in gel proteolysis, and comparative mass spectrometric analysis of peptide fragments. The lysines modified in free RT but protected from biotinylation in the nucleoprotein complex were readily revealed by this approach. Results of a control experiment examining the RT-DNA:DNA complex were in excellent agreement with the crystal structure data on the identical complex. Probing the RT-viral RNA:tRNA complex revealed that a majority of protein contacts are located in the primer-template binding cleft in common with the RT-DNA:DNA and RT-RNA:DNA species. However, our footprinting data indicate that the p66 fingers subdomain makes additional contacts to the viral RNA:tRNA specific for this complex and not detected with DNA:DNA. The protein footprinting method described herein has a generic application for high-resolution solution structural studies of multiprotein-nucleic acid contacts.
Amino Acid Sequence↗
3'-End polishing of the kinetoplastid spliced leader RNA is performed by SNIP, a 3'-->5' exonuclease with a Motley assortment of small RNA substrates.
In all trypanosomatids, trans splicing of the spliced leader (SL) RNA is a required step in the maturation of all nucleus-derived mRNAs. The SL RNA is transcribed with an oligo-U 3' extension that is removed prior to trans splicing. Here we report the identification and characterization of a nonexosomal, 3'-->5' exonuclease required for SL RNA 3'-end formation in Trypanosoma brucei. We named this enzyme SNIP (for snRNA incomplete 3' processing). The central 158-amino-acid domain of SNIP is related to the exonuclease III (ExoIII) domain of the 3'-->5' proofreading epsilon subunit of Escherichia coli DNA polymerase III holoenzyme. SNIP had a preference for oligo(U) 3' extensions in vitro. RNA interference-mediated knockdown of SNIP resulted in a growth defect and correlated with the accumulation of one- to two- nucleotide 3' extensions of SL RNA, U2 and U4 snRNAs, a five-nucleotide extension of 5S rRNA, and the destabilization of U3 snoRNA and U2 snRNA. SNIP-green fluorescent protein localized to the nucleoplasm, and substrate SL RNA derived from SNIP knockdown cells showed wild-type cap 4 modification, indicating that SNIP acts on SL RNA after cytosolic trafficking. Since the primary SL RNA transcript was not the accumulating species in SNIP knockdown cells, SL RNA 3'-end formation is a multistep process in which SNIP provides the ultimate 3'-end polishing. We speculate that SNIP is part of an organized nucleoplasmic machinery responsible for processing of SL RNA.
Animals↗
A historical perspective on RNA editing: how the peculiar and bizarre became mainstream.
The known examples of RNA editing now encompass a variety of alterations of RNA primary sequence that arise from base modifications, nucleotide insertions or deletions, and nucleotide replacements. Hence, the definition of RNA editing has evolved as new systems have been described. This chapter presents a historical perspective on some of the pivotal discoveries that helped direct the current avenues of research in the field of RNA editing.
Animals↗
Faithful and efficient translation of homologous and heterologous mRNAs in an mRNA-dependent cell-free system from Saccharomyces cerevisiae.
A cell-free protein synthesizing system from the yeast Saccharomyces cerevisiae has been optimized for the translation of both homologous yeast mRNA and for a number of heterologous eukaryotic mRNAs. A significant increase in protein synthesis was observed when K(OAc) rather than KCl was used as the source of K+ in the in vitro translation system. This was due primarily to an inhibitory effect oif Cl-. The polyamine putrescine hydrochloride stimulated protein synthesis only at low Mg2+ concentrations. Protein synthesis directed by both yeast mRNA and several eukaryotic mRNAs examined in the system was sensitive to the mRNA 5'-cap analogue, 7-methylguanosine 5'-monophosphate. One-dimensional and two-dimensional polyacrylamide gel analysis of polypeptides synthesized in response to yeast polysomal RNA demonstrated faithful translation in vitro. Translational control and post-translational modifications appear to operate normally in vitro. RNA from several eukaryotic viruses (brome mosaic virus, turnip yellow mosaic virus, and tobacco mosaic virus) were found to be faithfully translated in vitro yielding discrete polypeptides. Reticulocyte polysomal RNA directed the synthesis of a single protein that co-migrated with rabbit globin. The prokaryotic RNAs of Q beta and MS2 were translated with a very low efficiency. The yeast cell-free system programmed with yeast polysomal RNA provides an excellent model for the study of translational control in a eukaryote.
Animals↗
Identification of a high-affinity RNA-binding site for the human immunodeficiency virus type 1 Rev protein.
Expression of the structural proteins of human immunodeficiency virus type 1 requires the direct interaction of multiple copies of the viral Rev protein with its highly structured RNA target sequence, the Rev response element (RRE). Nucleotides critical for Rev monomer binding have been mapped by chemical interference to a single site flanking the base of an RNA helix (stem IIB) located within the 234-nucleotide RRE. Binding of additional Rev molecules to an RRE probe did not require any RNA primary sequence information detectable by modification interference beyond that required for binding of a single Rev protein molecule. A synthetic 29-nucleotide RNA molecule designed to incorporate nucleotides identified as critical for Rev binding retained the ability to bind Rev specifically and, therefore, represents a minimal Rev-binding site. We propose that Rev binding to the RRE initiates with the direct interaction of a Rev monomer with a high-affinity binding site located at the base of the IIB stem of the RRE. The subsequent formation of Rev multimers on the RRE appears, in contrast, primarily driven by specific protein-protein interactions.
Base Sequence↗
Towards a molecular genetic approach to Alzheimer's disease.
The current observations of a familial form of Alzheimer's disease and the alterations in the neurochemistry of Alzheimer tissue including neurotransmitter deficits, paired helical filament and RNA degradation suggest that the modification of specific genes may be responsible for the disease. These genes may be identified with the use of complementary DNA probes synthesized from normal and Alzheimer mRNA. In characterizing the gene expression in demented tissue, we have found that RNA from Alzheimer frontal cortex and hippocampus was partially degraded compared to RNA isolated from control. However, the polyadenylated RNA exhibited no obvious degradation. Similarly, polysome content of the Alzheimer tissue was lower than in control tissues. In addition, the Alzheimer polysomes were much less efficient in protein synthesis.
Alzheimer Disease↗
Synthesis of amine- and thiol-modified nucleoside phosphoramidites for site-specific introduction of biophysical probes into RNA.
For studies of RNA structure, folding, and catalysis, site-specific modifications are typically introduced by solid-phase synthesis of RNA oligonucleotides using nucleoside phosphoramidites. Here, we report the preparation of two complete series of RNA nucleoside phosphoramidites; each has an appropriately protected amine or thiol functional group. The first series includes each of the four common RNA nucleotides, U, C, A, and G, with a 2'-(2-aminoethoxy)-2'-deoxy substitution (i.e., a primary amino group tethered to the 2'-oxygen by a two-carbon linker). The second series encompasses the four common RNA nucleotides, each with the analogous 2'-(2-mercaptoethoxy)-2'-deoxy substitution (i.e., a tethered 2'-thiol). The amines are useful for acylation and reductive amination reactions, and the thiols participate in displacement and oxidative cross-linking reactions, among other likely applications. The new phosphoramidites will be particularly valuable for enabling site-specific introduction of biophysical probes and constraints into RNA.
Amides↗
A-to-I RNA editing remodels 5'-UTR initiation codons to tune translational output.
A-to-I RNA editing is a prevalent post-transcriptional modification in higher eukaryotes that converts adenosine to inosine within RNA molecules. Because inosine is interpreted as guanosine during translation, editing can alter codon identity and potentially influence translation initiation signals. Here, we examined whether A-to-I editing within the 5' untranslated region (5'-UTR) can remodel upstream initiation codons and thereby tune downstream translation. Using luciferase-based reporter systems, we show that AUA-to-AUI editing generates an initiation-competent inosine-containing codon, whereas AUG-to-IUG editing markedly attenuates initiation and can relieve uORF-mediated repression. Quantitative in vitro and cellular assays establish the initiation hierarchy AUA < AUI < AUG, with IUG exhibiting strongly reduced initiation efficiency. Importantly, AUI-mediated upstream initiation did not behave like a canonical AUG-initiated uORF in the tested contexts; its effect on downstream ORF translation was modest and context-dependent. Transcriptome-wide bioinformatic analysis identified endogenous human transcripts whose 5'-UTRs harbor editing sites compatible with initiation-codon gain or attenuation. Reporter validation using native 5'-UTR sequences supports the possibility that editing-dependent initiation-codon remodeling can tune translational output in living cells, particularly through AUG-to-IUG-mediated derepression. Together, these findings establish a reporter-based framework in which A-to-I editing can remodel 5'-UTR initiation codons, while highlighting the need for endogenous protein-level and native-locus validation to determine physiological relevance.
RNA Editing↗
[Inhibitory effect of various 3'-amino- and 3'-azido-3'-deoxyribonucleotide-5'-triphosphates on RNA synthesis, catalyzed by RNA polymerase of influenza type A virus and cellular RNA-polymerase].
Some new analogues of ribonucleoside-5'-triphosphates modified in 3'-ribose position and base [CTP (3'NH2), CTP (3'NH2) (5Me), CTP (3'N3) (5 Me), RvTP (3'N3)] have been synthesized. The inhibitions of RNA-synthesis catalyzed by the influenza A viral RNA-polymerase in cell free system and by the RNA-polymerase II from mice liver in the system of cellular nuclei by these reagents have been compared. All the studied preparations efficiently inhibited the RNA-synthesis in both cases. The inhibitors modified only in 3'-ribose position did not express specificity to any of RNA-polymerases tested, while some analogues having two modification in the molecule demonstrated the selective inhibition of RNA-synthesis directed by the influenza A viral RNA-polymerase [ara GTP (3'NH2), RvTP (3'N3')].
Animals↗
Ribonucleosides and RNA.
Landmark discoveries such as the autocatalytic cleavage activity of certain RNA molecules, as well as small oligoribonucletide ribozymes and later the in vitro evolution of novel bioactive oligoribonucleotides (SELEX), have created entire new fields of biochemical research. The discovery of SELEX has provided a method for producing high-affinity nucleic acid ligands with high binding specificity to important medicinal targets. Including modified nucleotides into RNA ligands derived from SELEX may yield improved RNA therapeutics. The chemistry of oligoribonucleotides in comparison to oligodeoxyribonucleotides has led to resurgent attention on the role of modified nucleotides in RNA structure and function. Such modifications are also employed to impart stability towards endonuclease degradation on oligoribonucleotides.
Base Sequence↗
Modification of protein synthetic components by aflatoxin B1.
Molecular sites of perturbation by the hepatocarcinogen aflatoxin B1 (AFB1) in the protein synthesis initiation complex were assessed using isolated hepatocytes and a cell-free activating system containing microsomes and cytoplasmic ribonucleoprotein complexes (cRPC). Ribosomal proteins showed no detectable modification by the toxin in either system. With hepatocytes, initiation factors demonstrated only slight modification by AFB1. RNAs from both hepatocytes and the cell-free system with microsomes and cRPC were modified, with poly(A)-containing RNA exhibiting at least a 5-fold higher modification than poly(A)-lacking RNA. The poly(A)-lacking RNAs were modified in the order 28S rRNA greater than 18S rRNA greater than 5-6S rRNA greater than 4S tRNA. Guanine was the target base of AFB1, but only 10% of the AFB1-GMP adducts were on guanines located in a poly(G) region. These results suggest that guanine modification in RNAs may be responsible for the observed inhibition of translational initiation by AFB1 to a greater extent than modification of either ribosomal intrinsic or associated proteins.
Aflatoxin B1↗