Preparation, purification and analyses of thirteen alkali-stable dinucleotides from yeast ribonucleic acid

Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life

Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.

Epitranscriptomic marks: Emerging modulators of RNA virus gene expression

Epitranscriptomics, the study of posttranscriptional chemical moieties placed on RNA, has blossomed in recent years. This is due in part to the emergence of high‐throughput detection methods as well as the burst of discoveries showing biological function of select chemical marks. RNA modifications have been shown to affect RNA structure, localization, and functions such as alternative splicing, stabilizing transcripts, nuclear export, cap‐dependent and cap‐independent translation, microRNA biogenesis and binding, RNA degradation, and immune regulation. As such, the deposition of chemical marks on RNA has the unique capability to spatially and temporally regulate gene expression. The goal of this article is to present the exciting convergence of the epitranscriptomic and virology fields, specifically the deposition and biological impact of N7‐methylguanosine, ribose 2′‐O‐methylation, pseudouridine, inosine, N6‐methyladenosine, and 5‐methylcytosine epitranscriptomic marks on gene expression of RNA viruses.

This article is categorized under:

RNA in Disease and Development > RNA in Disease

RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications

Detection and Analysis of RNA Ribose 2'-O-Methylations: Challenges and Solutions

Ribose 2'-O-methylation is certainly one of the most common RNA modifications found in almost any type of cellular RNA. It decorates transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs) (and most probably small nucleolar RNAs, snoRNAs), as well as regulatory RNAs like microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and finally, eukaryotic messenger RNAs (mRNAs). Due to this exceptional widespread of RNA 2'-O-methylation, considerable efforts were made in order to precisely map these numerous modifications. Extensive studies of RNA 2'-O-methylation were also stimulated by the discovery of C/D-box snoRNA-guided machinery, which insures site-specific modification of hundreds 2'-O-methylated residues in archaeal and eukaryotic rRNAs and some other RNAs. In this brief review we discussed both traditional approaches of RNA biochemistry and also modern deep sequencing-based methods, used for detection/mapping and quantification of RNA 2'-O-methylations.

RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions

Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.

The preparation and analysis of a new trinucleotide from yeast ribonucleic acid, containing two adjacent 2'-O-methylpentose residues

Quantities of the order of 10mg of three alkali-stable trinucleotides were prepared from yeast ribonucleic acid. Analyses showed that they were of the type N1m-N2m-N3p, where m signifies 2'-O-methylation of the pentose residue. One, Am-Um-Gp, is newly described.

Apiose and mono-O-methyl sugars as minor constituents of the leaves of deciduous trees and various other species

1. Leaves of a number of species were hydrolysed with aqueous sulphuric acid and the resulting mixtures of sugars were fractionated by chromatography on activated charcoal. Paper chromatography of the fractions showed the presence in all the hydrolysates of minor constituents with R(F) values similar to or greater than those of the common hexoses and pentoses. 2. Two of these were identified as 2-O-methylxylose and 2-O-methylfucose. Estimates of the amounts present in whole leaves, and in fractions prepared from them, showed that they were associated with the hemicelluloses. 3. A third constituent was identified, by the formation of its di-isopropylidene derivative, as apiose. It also was associated chiefly with the hemicellulose fraction; none could be found in aqueous extracts from leaves of Tilia vulgaris, nor in aqueous extracts of Zostera marina, in which apiose is a major constituent of the water-insoluble polysaccharide. 4. A further constituent, after further purification by preparative paper chromatography, was tentatively identified, by gas-liquid chromatography of derivatives, as 3-O-methylgalactose, and was probably accompanied by small amounts of 4-O-methylgalactose. 5. These observations confirm the widespread occurrence of 2-O-methylxylose, 2-O-methylfucose and apiose, but 3-O-methylgalactose was hitherto known only in slippery-elm mucilage, and 4-O-methylgalactose in soil polysaccharides. Some experiments on the digestion of leaf hemicellulose fractions by snail crop-juice suggested that the mono-O-methyl sugars might confer resistance to enzymic degradation.